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PDB ID Mentions in PubMed Central Article count: 70

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle.

(2005) Nucleic Acids Res 33

PubMed: 15951514 | PubMedCentral: PMC1150222 | DOI: 10.1093/nar/gki663

The single remaining Mn 2+ binding site, at the base pair location of −5, was observed in the 1.9 Å structure of Xla -NCP (PDB code 1KX5) ( 11 , 15 ).

Four chloride ions were identified, as two peaks of the H3-α3 helices near the center of the DNA and two peaks of the H2B-α3 helix and H2A-α2 helix, in agreement with the Xla -NCP structure at 1.9 Å resolution (PDB code 1KX5) ( 11 ).

Publication Year: 2005


Asymmetry in the burial of hydrophobic residues along the histone chains of eukarya, archaea and a transcription factor.

(2005) BMC Struct Biol 5

PubMed: 16242031 | PubMedCentral: PMC1283977 | DOI: 10.1186/1472-6807-5-20

Figure 1 highlights the c-terminal regions of the A and E chains of the H3 histones of the 1KX5 structure involved in the four-fold helical coupling that binds the dimers of the tetramer.

Histones from the Xenopus laevis [ 26 ] (PDB id 1KX5), Gallus gallus [ 27 ] (PDB id 1EQZ) and Saccharomyces cerevisae [ 28 ] (PDB id 1ID3) species had been used in the calculations.

Figure 6 Ribbon diagrams of the homologous tetrameric histone structures from (a) Drosophila melanogaster (PDB id 1TAF) (b) Xenopus laevis (PDB id 1KX5) (c) Methanopyrus kandleri (PDB id 1F1E).

Figure 7 Combinatorial Extension (CE) alignment of the tetrameric histone structures of (a) Methanopyrus kandleri (PDB id 1F1E) and (b) Drosophila melanogaster (PDB id 1TAF) with Xenopus laevis (PDB id 1KX5).

Publication Year: 2005


Attenuation of DNA charge transport by compaction into a nucleosome core particle.

(2006) Nucleic Acids Res 34

PubMed: 16595797 | PubMedCentral: PMC1428796 | DOI: 10.1093/nar/gkl030

Figure 5 (A) Crystal structure of the NCP (Protein Data Bank Accession no. 1KX5) with 147 bp of DNA (nucleobases = purple, sugar-phosphate backbone = blue) modified to include a 10 bp extension and a ... ovalently attached AQ (green) end-capped onto the DNA.

Publication Year: 2006


Multiple independent evolutionary solutions to core histone gene regulation.

(2006) Genome Biol 7

PubMed: 17184543 | PubMedCentral: PMC1794435 | DOI: 10.1186/gb-2006-7-12-r122

A three-dimensional structure of the nucleosome core, PDB ID:1KX5 [ 62 ], used for comparison was taken from the RCSB Protein Data Bank [ 63 ].

Publication Year: 2006


A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

(2007) Genome Biol 8

PubMed: 17521420 | PubMedCentral: PMC1929158 | DOI: 10.1186/gb-2007-8-5-r90

(d) Structure of a histone dimer (red and light yellow) bound to DNA (green and cyan) [84] (PDB: 1kx5).

Publication Year: 2007


An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length.

(2007) PLoS One 2

PubMed: 17849006 | PubMedCentral: PMC1963316 | DOI: 10.1371/journal.pone.0000877

Based on this classification, we built a library of 16 template fiber structures ranging from one to five start helices, by placing the 30 NCP crystal structures (1KX5) [22] according ... o the measured fibers dimensions.

Publication Year: 2007


Sequence-dependent DNA deformability studied using molecular dynamics simulations.

(2007) Nucleic Acids Res 35

PubMed: 17766249 | PubMedCentral: PMC2094071 | DOI: 10.1093/nar/gkm627

As a preliminary test, we evaluated the fitness of co-crystallized DNA sequences against histones ( 31 ) (PDB code: 1kx3, 1kx4 and 1kx5) by threading the DNA sequences on each of the three nucleosome ... ore structures.

Evaluation of fitness for nucleosome core structure DNA sequences were threaded on known nucleosome core structures (PDB codes: 1kx3, 1kx4 and 1kx5) ( 31 ), and the fitness of each of the three co-crystallized DNA sequences to each of the three structures was evaluated in the form of a Z-score that was calculated as the deviation of the energy of the target sequence from the energy distribution of random DNA sequences.

Publication Year: 2007


Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.

(2007) Nucleic Acids Res 35

PubMed: 17986463 | PubMedCentral: PMC2190717 | DOI: 10.1093/nar/gkm890

The supercoiled DNA was modeled using the X-ray structure of the nucleosome NP147 centered around THY50 (PDB code: 1kx5) ( 14 ), with nucleic acids mutated to the corresponding sequence of p53REs.

Publication Year: 2007


DNA conformations and their sequence preferences.

(2008) Nucleic Acids Res 36

PubMed: 18477633 | PubMedCentral: PMC2441783 | DOI: 10.1093/nar/gkn260

The backbone in Structure 1KX5 ( 89 ) exhibits a fairly regular periodic alteration of BI and BII conformers, occasionally varied at points of direct protein/DNA contacts by more deformed B-type confo... mers, characterized by flipped α + 1 and γ + 1 torsions (‘switched BI’, Clusters 113–117, Table 4 and Supplementary Table T2 ) and by several residues with scattered values of ζ and α + 1.

Dinucleotide conformations in the crystal structure of the histone-core particle 1KX5 ( 89 ).

The PDB codes of the structures used in the analysis Structure Type PDB Codes Noncomplexed A-DNA ( 46 ) 118d, 137d, 138d, 160d, 1d78, 1d79, 1dnz, 1kgk, 1m77, 1ma8, 1mlx, 1nzg, 1vj4, 1xjx, 1z7i, 1zex, 1zey, 1zf1, 1zf6, 1zf8, 1zf9, 1zfa, 213d, 243d, 260d, 295d, 2d94, 317d, 338d, 344d, 345d, 348d, 349d, 368d, 369d, 370d, 371d, 395d, 396d, 399d, 414d, 440d, 9dna, dh010, adh012, adh034 Noncomplexed B-DNA ( 72 ) 122d, 123d, 158d, 183d, 196d, 1bd1, 1bna, 1cw9, 1d23, 1d3r, 1d49, 1d56, 1d61, 1d8g, 1d8x, 1dou, 1dpn, 1edr, 1ehv, 1en3, 1en8, 1en9, 1ene, 1enn, 1fq2, 1g75, 1i3t, 1ikk, 1j8l, 1jgr, 1l4j, 1l6b, 1m6g, 1n1o, 1nvn, 1nvy, 1p4y, 1p54, 1s23, 1s2r, 1sgs, 1sk5, 1ub8, 1ve8, 1zf0, 1zf3, 1zf4, 1zf5, 1zf7, 1zfb, 1zff, 1zfg, 232d, 251d, 2d25, 307d, 355d, 3dnb, 403d, 423d, 428d, 431d, 436d, 454d, 455d, 456d, 460d, 463d, 476d, 477d, 5dnb, 9bna DNA/drug and DNA/ protein complexes, Z-DNA, quadruplexes (329) 110d, 115d, 131d, 145d, 151d, 152d, 159d, 181d, 182d, 184d, 190d, 191d, 1a1g, 1a1h, 1a1i, 1a1k, 1a2e, 1a73, 1aay, 1ais, 1azp, 1b94, 1b97, 1bf4, 1bqj, 1brn, 1c8c, 1cdw, 1ckq, 1cl8, 1cn0, 1d02, 1d11, 1d14, 1d15, 1d21, 1d22, 1d2i, 1d32, 1d37, 1d38, 1d40, 1d41, 1d45, 1d48, 1d53, 1d54, 1d58, 1d67, 1d76, 1d90, 1d9r, 1da0, 1da2, 1da9, 1dc0, 1dc1, 1dcg, 1dcr, 1dcw, 1dfm, 1dj6, 1dl8, 1dn4, 1dn5, 1dn8, 1dnf, 1dp7, 1dsz, 1e3o, 1egw, 1em0, 1emh, 1eo4, 1eon, 1esg, 1eyu, 1f0v, 1fd5, 1fdg, 1fhz, 1fiu, 1fms, 1fn1, 1fn2, 1g2f, 1g9z, 1gtw, 1gu4, 1h6f, 1hcr, 1hlv, 1hwt, 1hzs, 1i0t, 1i3w, 1ick, 1ign, 1ih4, 1ih6, 1imr, 1ims, 1j59, 1j75, 1jb7, 1jes, 1jft, 1jh9, 1jk1, 1jk2, 1jpq, 1jtl, 1juc, 1jux, 1jx4, 1k3w, 1k3x, 1k9g, 1kbu, 1kci, 1kx3, 1kx5, 1l1h, 1l1t, 1l1z, 1l3l, 1l3s, 1l3t, 1l3u, 1l3v, 1lat, 1lau, 1ljx, 1llm, 1lmb, 1m07, 1m19, 1m3q, 1m5r, 1m69, 1m6f, 1mf5, 1mj2, 1mjm, 1mjo, 1mjq, 1mnn, 1mus, 1mw8, 1nh2, 1njw, 1njx, 1nk0, 1nk4, 1nk7, 1nk8, 1nk9, 1nkc, 1nke, 1nkp, 1nnj, 1nqs, 1nr8, 1nt8, 1nvp, 1o0k, 1omk, 1orn, 1p20, 1p3i, 1p3l, 1p71, 1per, 1pfe, 1ph4, 1ph6, 1ph8, 1pji, 1pjj, 1puf, 1pup, 1puy, 1q3f, 1qda, 1qn3, 1qn4, 1qn5, 1qn6, 1qn8, 1qn9, 1qna, 1qnb, 1qne, 1qum, 1qyk, 1qyl, 1qzg, 1r2z, 1r3z, 1r41, 1r68, 1rff, 1rh6, 1rnb, 1rpe, 1rqy, 1run, 1s1k, 1s1l, 1s32, 1ssp, 1suz, 1sx5, 1sxq, 1t9i, 1tdz, 1tez, 1tro, 1u1p, 1u1q, 1u1r, 1u4b, 1ue2, 1ue4, 1uhy, 1v3n, 1v3o, 1v3p, 1vzk, 1w0u, 1wd0, 1wte, 1wto, 1wtp, 1wtq, 1wtr, 1wtv, 1xa2, 1xam, 1xc9, 1xjv, 1xo0, 1xuw, 1xux, 1xvn, 1xvr, 1xyi, 1ytb, 1ytf, 1zez, 1zf2, 1zna, 200d, 210d, 211d, 212d, 215d, 221d, 224d, 234d, 235d, 236d, 241d, 242d, 244d, 245d, 254d, 258d, 276d, 277d, 278d, 279d, 284d, 288d, 292d, 293d, 2bdp, 2bop, 2cgp, 2crx, 2dcg, 2des, 2hap, 2hdd, 2nll, 2or1, 2pvi, 304d, 306d, 308d, 313d, 314d, 331d, 334d, 336d, 351d, 352d, 360d, 362d, 366d, 367d, 383d, 385d, 386d, 3bam, 3bdp, 3cro, 3crx, 3hts, 3pvi, 400d, 417d, 427d, 432d, 441d, 442d, 443d, 452d, 453d, 465d, 467d, 473d, 481d, 482d, 4bdp, adh013, zdf013, zdfb03, zdfb06 The DNA conformational space was investigated at the level of a dinucleotide unit with its 5′-end phosphate group removed; it was described by six backbone torsion angles between γ and δ + 1, plus two χ angles characterizing the glycosidic bond ( Figure 1 ).

Publication Year: 2008


Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer.

(2008) Proteins 71

PubMed: 17957772 | PubMedCentral: PMC2443955 | DOI: 10.1002/prot.21720

The Xla-NCP147 structure (pdb id 1KX5) minus the N-terminal histone tail residues was used as a starting model.

Publication Year: 2008


Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46.

(2008) Structure 16

PubMed: 18571423 | PubMedCentral: PMC2572730 | DOI: 10.1016/j.str.2008.05.006

(C) Comparison of the interactions of Ile-34, Leu-37, and Ala-38 in helix 1 of histone H4 with (i) the N-terminal helix of RbAp46 in the RbAp46/histone H4 peptide structure, (ii) α helices 2 o... histone H3 and H4 in one (of the two) H3/H4 dimer in the nucleosome core particle ( Davey et al., 2002 ; PDB code: 1KX5 ), and (iii) α helices 2 of histone H3 and H4 in the ASF1-histone H3/H4 complex ( English et al., 2006; Natsume et al., 2007 ; PDB code: 2HUE ).

Publication Year: 2008


Nucleosomes can invade DNA territories occupied by their neighbors.

(2009) Nat Struct Mol Biol 16

PubMed: 19182801 | PubMedCentral: PMC2675935 | DOI: 10.1038/nsmb.1551

The models are based on the high-resolution crystal structure of the NCP 1KX5.

Publication Year: 2009


Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs.

(2009) BMC Struct Biol 9

PubMed: 19393049 | PubMedCentral: PMC2687451 | DOI: 10.1186/1472-6807-9-24

The PDB id's correspond to the following biological molecules: 1KX5 – Nucleosome core particle, 4CRX – CRE recombinase protein-bound DNA, 1J59 – Catabolic Activator Protein (CA... )-bound DNA, 1DDN -Diphtheria tox repressor-bound DNA, 1T9J – Endonuclease-bound DNA, 1RIO – lambda CI-NTD-sigma-region4-bound DNA, 1APL – MAT alpha2 homeodomain-bound DNA.

It is also interesting to note that the ROC calculated for the 76 basepair fragments in 1KX3 and 1KX5 are 39.8 Å and 39.4 Å respectively, while that for a 2.8 Å resolution structure (1AOI [ 89 ]) is calculated as 41.5 Å, indicating that the DNA in different nucleosome structures has small variations in curvature.

A segment of the nucleosome structure (1KX5 [ 86 ]) consisting of 30 basepairs gives a d/l local value of 0.77 and a ROC value of 37.9 Å, with circle fit standard deviation of 0.6 Å, indicating that the measures used are quite adequate to define curvature of DNA molecules of this length.

Cfit Lfit Cfit/Lfit Value Position 1KX5 30 15.1 10.5 51.9 A 10 A 11 A 12 126.7 0.77 37.9 0.6 20.0 0.03 C 0.1 1KX3 30 19.3 9.9 37.4 G 3 C 4 A 5 129.5 0.77 37.8 0.7 10.5 0.07 C -4.7 1N3F 22 11.7 8.0 32.6 G 12 A 13 G 14 23.4 0.97 65.1 0.5 3.2 0.16 C -0.5 1T9J 22 13.3 9.3 32.0 C 6 G 7 T 8 26.2 0.97 65.9 0.6 13.1 0.05 C 12.5 1G9Z 22 14.8 11.4 35.9 T 8 C 9 G 10 22.9 0.97 68.3 0.6 13.0 0.05 C -24.5 1T9I 22 12.1 9.3 28.6 C 6 G 7 T 8 23.2 0.98 66.3 0.5 13.7 0.04 C 15.0 1OWF 20 16.9 15.5 56.7 T 11 T 12 G 13 85.0 0.81 NA 1.2 13.2 0.09 U NA 1CYQ 18 14.0 4.4 26.5 A 13 G 14 A 15 55.0 0.90 NA 2.4 5.4 0.44 U NA 1A73 18 14.1 4.5 23.0 A 13 G 14 A 15 56.7 0.91 NA 2.3 5.3 0.43 U NA 1ZS4 23 9.4 5.0 18.1 T 12 G 13 T 14 8.1 0.99 NA 0.8 1.5 0.53 U NA 1H6F 20 8.3 4.7 17.5 T 15 G 16 T 17 26.2 0.99 NA 4.4 1.1 4.00 U NA The other specifications are as detailed in the caption to table 7.

Cfit Lfit Cfit/Lfit Value Position 1KX5 30 15.1 10.5 51.9 A 10 A 11 A 12 126.7 0.77 37.9 0.6 20.0 0.03 C 0.1 1J59 28 25.3 16.2 66.5 T 9 G 10 A 11 98.5 0.85 47.2 0.7 21.4 0.03 C -41.9 1RUN 28 30.4 17.1 71.1 T 9 G 10 A 11 109.7 0.85 47.8 0.6 22.2 0.03 C -50.6 1CGP 26 19.1 18.9 65.9 G 7 T 8 G 9 72.4 0.86 48.2 0.8 17.9 0.04 C -51.1 1BL0 20 10.5 6.1 25.0 A 6 G 7 C 8 38.8 0.94 47.0 0.7 3.6 0.19 C -68.9 1HLV 19 10.0 7.6 30.1 G 15 G 16 G 17 39.3 0.95 54.6 0.6 3.3 0.18 C -129.0 1APL 18 11.8 7.3 33.0 A 16 C 17 G 18 3.7 0.99 NA 4.9 0.9 5.44 L NA 1K78 23 9.1 3.2 15.6 T 19 G 20 G 21 15.9 1.00 NA 2.4 1.0 2.40 L NA 4CRX 32 11.8 12.2 56.5 A 17 T 18 G 19 76.3 0.82 NA 3.4 9.1 0.37 U NA 1GDT 32 15.4 13.0 60.3 T 14 T 15 A 16 40.2 0.87 NA 1.6 14.5 0.11 U NA 1MNM 23 11.8 7.8 26.8 G 13 A 14 A 15 58.7 0.89 NA 1.7 5.4 0.31 U NA 1JE8 18 23.0 13.0 49.6 T 2 A 3 C 4 56.9 0.93 NA 1.1 5.0 0.22 U NA 1DDN 23 8.8 4.4 19.1 T 13 T 14 A 15 36.0 0.95 NA 7.7 2.5 3.08 U NA 1L3L 18 9.0 5.9 19.7 C 14 A 15 C 16 32.5 0.96 NA 1.5 1.6 0.94 U NA 1U78 23 10.6 12.3 51.1 T 10 A 11 G 12 41.3 0.97 NA 1.4 19.6 0.07 U NA 1Z9C 24 10.0 5.9 23.9 T 11 A 12 T 13 3.4 0.97 NA 6.1 2.0 3.05 U NA 1H88 23 7.4 4.5 16.8 C 8 A 9 A 10 12.3 0.98 NA 1.6 7.8 0.21 U NA 1D5Y 18 8.9 5.7 21.6 C 15 A 16 A 17 10.6 0.98 NA 2.6 2.0 1.30 U NA 1K61 18 8.8 6.1 22.3 T 4 A 5 A 6 6.6 0.99 NA 1.3 7.1 0.18 U NA 1DU0 18 6.3 4.0 15.2 C 15 C 16 T 17 10.1 0.99 NA 0.6 2.9 0.21 U NA 1RIO 25 14.8 8.7 34.1 C 8 C 9 G 10 16.1 0.99 NA 0.6 2.7 0.22 U NA 6PAX 22 11.8 7.1 25.6 A 8 C 9 G 10 20.4 0.99 NA 0.6 2.1 0.29 U NA 2HDD 18 10.7 5.4 23.3 T 12 C 13 C 14 22.9 0.99 NA 1.2 1.8 0.67 U NA 1HDD 18 10.9 4.1 19.9 G 3 C 4 C 5 1.9 0.99 NA 2.6 1.4 1.86 U NA 3HDD 18 6.5 3.7 14.4 G 8 T 9 A 10 8.3 0.99 NA 3.0 1.4 2.14 U NA 1JT0 26 10.4 5.9 22.1 A 23 T 24 A 25 29.8 0.99 NA 9.1 1.1 8.27 U NA 1F4K 19 7.9 5.1 20.2 T 3 G 4 A 5 24.8 1.00 NA 0.8 2.4 0.33 U NA 1MDM 23 9.2 4.7 20.8 A 6 G 7 A 8 15.6 1.00 NA 1.7 1.1 1.55 U NA 1HF0 20 10.5 7.3 30.7 T 6 G 7 A 8 28.6 1.01 NA 1.4 0.9 1.56 U NA The calculation of successive bending angles, end-to-end bending angle, d/l local , Radius of Curvature (ROC), RMSD for circle fit (Cfit) and line fit (Lfit) and torsion angle for out-of-plane component of bending have been described in the 'Methods' section.

Publication Year: 2009


Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.

(2009) Nucleic Acids Res 37

PubMed: 19474339 | PubMedCentral: PMC2703980 | DOI: 10.1093/nar/gkp358

The images include: (i) composite block/tube/backbone representations of the type used to illustrate nucleosomal DNA ( 31 ) (PDB ID: 1KX5) in Figure 3 a; (ii) stacking diagrams of associated base pair... like that shown for neighboring C·G and A·U pairs in Figure 3 b; and (iii) composite block/ribbon/backbone representations of structural ensembles, such as the NMR-based models of the 5S RNA-TFIIIA complex ( 32 ) (PDB ID: 2HGH) depicted in Figure 3 c. Figure 3.

( a ) Color-coded composite block/backbone/tube representation of the DNA in the currently best-resolved nucleosome core-particle structure ( 31 ) (PDB ID: 1KX5).

Publication Year: 2009


Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

(2009) Nucleic Acids Res 37

PubMed: 19509309 | PubMedCentral: PMC2724288 | DOI: 10.1093/nar/gkp475

X146 and X147 are 146 and 147 bp DNA sequences from nucleosome crystal structures 1aoi ( 10 ) and 1kx5 ( 2 ).

Geometry minimization is essential for these predictions—the same calculations are much less successful if DNA geometries are taken from the nucleosome crystal structure (1kx5) ( 14 ), or if DNA is threaded along an ideal superhelix [ Supplementary Figure 4 ; ( 15 )].

( b ) Elastic energy components for all possible dinucleotides substituted into the 1kx5 crystal structure at position 109 where the DNA conformation is kinked ( Figure 2 ) ( 2 ).

The 146- and 147-bp long DNAs analyzed in X-ray crystallographic studies of nucleosomes (PDB codes 1aoi and 1kx5, respectively) were prepared as described ( 26 ) using clones supplied by Professors K. Luger and T.J. Richmond, respectively.

Therefore, one way to validate DNABEND is to predict the DNA conformation in the high-resolution (1.9 Å) nucleosome crystal structure [( 2 ); PDB code 1kx5], using only DNA sequence as input.

Six dinucleotide degrees of freedom in the crystal structure of the nucleosome core particle [( 2 ); PDB code: 1kx5] (blue), in the minimum energy structure obtained using 1kx5 DNA sequence as input to DNABEND (red) and in the ideal superhelix with no energy relaxation (green).

We fit w to maximize the average correlation coefficient between the distributions of geometric parameters observed in the high-resolution crystal structure of the nucleosome core particle [PDB code 1kx5; ( 2 )] and the corresponding DNABEND predictions ( Figure 2 ).

( a ) Position-dependent sequence specificity in the nucleosomal DNA revealed by the energetic analysis of dinucleotides substituted into the crystal structure of the nucleosome core particle [PDB code: 1kx5; ( 2 )] All possible dinucleotides were introduced at every position into the 147 bp nucleosomal site using DNA dihedral angles from the native dinucleotide, and DNA elastic energy was computed for every sequence variant.

Publication Year: 2009


The role of DNA shape in protein-DNA recognition.

(2009) Nature 461

PubMed: 19865164 | PubMedCentral: PMC2793086 | DOI: 10.1038/nature08473

Figure 4 Minor groove shape recognition in the nucleosome (a) Correlation of minor groove width of the nucleosome core particle (PDB code 1kx5) 24 (blue) and electrostatic potential (red).

Arginine-minor groove interactions in the nucleosome Figure 4a plots minor groove width and electrostatic potential along the DNA sequence of the nucleosome core particle containing recombinant histones and a 147 base pair DNA fragment (PDB code 1kx5) 24 .

Publication Year: 2009


Intrinsic flexibility of B-DNA: the experimental TRX scale.

(2010) Nucleic Acids Res 38

PubMed: 19920127 | PubMedCentral: PMC2817485 | DOI: 10.1093/nar/gkp962

Therefore, the NCP DNA structures analyzed here are those from entries 1KX3, 1M19 and 1KX5.

Roll (°) profile along the DNA sequence in nucleosome X-ray structure 1KX5.

Our analysis of several high resolution NCP X-ray structures [PDB codes 1KX3 ( 59 ), 1M19 ( 60 ) and 1KX5 ( 59 )] shows that positive and negative rolls are mainly associated to BI and BII phosphates, respectively ( Figure 5 for 1KX5).

Numerous nucleosome core particle (NCP) X-ray structures are available, but, to benefit from reliable structural details, we examined only the structures with resolution ≤2.5 Å, crystallized without histone mutants or groove ligands [PDB codes: 1EQZ ( 58 ), 1KX5 and 1KX3 ( 59 ), 1M19 ( 60 ), 2CV5 ( 61 )].

Publication Year: 2010


A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation.

(2009) Mol Cell 36

PubMed: 19818718 | PubMedCentral: PMC2856916 | DOI: 10.1016/j.molcel.2009.07.027

The figure was created using the PDB file 1KX5 and PyMOL ( http://www.pymol.org ).

The figure was created using the PDB file 1KX5 and PyMOL ( http://www.pymol.org ).

Publication Year: 2009


Chromatin fiber dynamics under tension and torsion.

(2010) Int J Mol Sci 11

PubMed: 20480035 | PubMedCentral: PMC2871131 | DOI: 10.3390/ijms11041557

Insert: nucleosome crystal structure (from 1kx5 PDB coordinates).

Publication Year: 2010


Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

(2010) PLoS Comput Biol 6

PubMed: 20628623 | PubMedCentral: PMC2900294 | DOI: 10.1371/journal.pcbi.1000834

3D structure visualization The 3D visualizations of the nucleosome core particle shown in Figure 2 were created using PyMol [47] and PolyView-3D [48] and PDB [4... ] structure 1KX5 [50] .

Publication Year: 2010


UV damage in DNA promotes nucleosome unwrapping.

(2010) J Biol Chem 285

PubMed: 20562439 | PubMedCentral: PMC2924050 | DOI: 10.1074/jbc.M110.140087

The NCP structure was generated from the crystal structure with Protein Data Bank code 1KX5 ( 39 ).

Publication Year: 2010


Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y.

(2010) J Cell Biol 190

PubMed: 20819935 | PubMedCentral: PMC2935562 | DOI: 10.1083/jcb.201002043

1kx5 .

Publication Year: 2010


Molecular modeling of mechanosensory ion channel structural and functional features.

(2010) PLoS One 5

PubMed: 20877470 | PubMedCentral: PMC2943245 | DOI: 10.1371/journal.pone.0012814

The structure of the homologous region comprises a 14-residue loopy region, which adopts different conformations in the two crystallographic studies available (1KX5 chain B and 1EQZ chain D).

Publication Year: 2010


The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres.

(2010) Nature 467

PubMed: 20739937 | PubMedCentral: PMC2946842 | DOI: 10.1038/nature09323

b , Overlay of (CENP-A/H4) 2 with (H3/H4) 2 (PDB ID 1KX5 15 ) was done with a secondary structure mapping (SSM) algorithm performed with one CENP-A molecule and one H3 molecule from each complex.

Crystallographic data were collected at Argonne National Laboratory and Advanced Light Source and one chain of H3 and one chain of H4 from the crystal structure of nucleosome (PDB ID 1KX5 15 ) were used as a search model for molecular replacement.

One chain of H3 and one chain of H4 from the crystal structure of nucleosome (PDB ID 1KX5 15 ) (or the structure of trypsinized (CENP-A/H4) 2 in the case of the engineered truncated version) were used as a search model for molecular replacement with PHASER 31 .

Publication Year: 2010


Perturbations in nucleosome structure from heavy metal association.

(2010) Nucleic Acids Res 38

PubMed: 20494975 | PubMedCentral: PMC2952864 | DOI: 10.1093/nar/gkq420

The histone–DNA model of NCP147 ( pdb code 1KX5; 17) was used for structure solution by molecular replacement.

Publication Year: 2010


Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures.

(2010) Nucleic Acids Res 38

PubMed: 20647418 | PubMedCentral: PMC2978337 | DOI: 10.1093/nar/gkq506

Similar pitch-controlling steps with the same types of ‘kink-and-slide’ arrangements occur at steps ±17 (the AG:CT dimer at SHL ±1.5) in the 147-bp nucleosome structure... (PDB ID: 1KX5) ( 26 ).

Publication Year: 2010


Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding.

(2010) PLoS Genet 6

PubMed: 21170357 | PubMedCentral: PMC3000355 | DOI: 10.1371/journal.pgen.1001234

Top: Histone H2A extracted from the crystal structure of the nucleosome core particle (1kx5) [58] .

Publication Year: 2010


Identification of lysine 37 of histone H2B as a novel site of methylation.

(2011) PLoS One 6

PubMed: 21249157 | PubMedCentral: PMC3020972 | DOI: 10.1371/journal.pone.0016244

The nucleosomal representation was generated using open-source PyMOL software (PyMOL 0.99rev10, DeLan Scientific LCC) with structural data taken from [100] (PDB file 1kx5).

Publication Year: 2011


An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression.

(2011) BMC Struct Biol 11

PubMed: 21208404 | PubMedCentral: PMC3031206 | DOI: 10.1186/1472-6807-11-1

Autocorrelation values for the rotational parameters roll and twist, and the translational parameter slide, for the six structures with PDB id's 1KX4 , 2NZD , 2F8N , 1KX3 , 1P3I and 1KX5 , correspondi... g to sequences 1, 2, 3, 4, 5 and 6 respectively.

PDB id d/l local I max /I min I m a x + I m i d I m i n ROC (Å) 1KX4 0.707 (0.018) 5.9 (0.5) 11.1 (1.1) 41.9 (2.0) 2NZD 0.707 (0.020) 5.8 (0.5) 11.0 (1.0) 41.8 (2.0) 1U35 0.710 (0.017) 5.9 (0.5) 11.1 (1.1) 42.0 (1.9) 2F8N 0.714 (0.017) 5.9 (0.5) 11.1 (1.1) 41.9 (2.0) 1AOI 0.710 (0.019) 5.9 (0.5) 11.0 (1.0) 42.0 (2.0) 1KX3 0.707 (0.020) 5.9 (0.5) 11.0 (1.0) 41.7 (2.0) 2CV5 0.708 (0.017) 5.9 (0.5) 11.1 (1.0) 41.9 (1.9) 1EQZ 0.712 (0.018) 5.9 (0.5) 11.1 (1.0) 41.8 (2.0) 1F66 0.708 (0.016) 5.8 (0.5) 11.0 (1.0) 41.9 (2.1) 1M18 0.713 (0.017) 5.9 (0.5) 11.1 (1.0) 42.2 (2.0) 1M19 0.716 (0.017) 6.0 (0.5) 11.2 (1.1) 42.0 (1.9) 1M1A 0.712 (0.017) 5.9 (0.5) 11.1 (1.0) 42.0 (1.8) 1P34 0.708 (0.019) 5.9 (0.5) 11.1 (1.1) 42.0 (2.1) 1P3A 0.708 (0.019) 5.9 (0.5) 11.0 (1.0) 41.9 (2.0) 1P3B 0.710 (0.019) 5.9 (0.5) 11.1 (1.0) 41.8 (2.0) 1P3F 0.710 (0.019) 5.9 (0.5) 11.1 (1.0) 41.8 (2.0) 1P3G 0.709 (0.019) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1P3I 0.708 (0.019) 5.9 (0.5) 11.1 (1.0) 41.9 (2.0) 1P3K 0.705 (0.020) 5.9 (0.5) 11.0 (1.0) 41.9 (2.0) 1P3L 0.710 (0.019) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1P3M 0.711 (0.020) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1P3O 0.708 (0.020) 5.9 (0.5) 11.0 (1.0) 41.9 (2.0) 1P3P 0.709 (0.019) 5.9 (0.5) 11.1 (1.0) 41.9 (2.0) 1S32 0.709 (0.019) 5.9 (0.4) 11.0 (0.9) 41.9 (1.9) 1ZLA 0.708 (0.019) 5.9 (0.5) 11.0 (1.0) 41.8 (2.0) 2NQB 0.708 (0.020) 5.8 (0.5) 11.0 (1.1) 41.9 (2.1) 3C1B 0.706 (0.019) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1KX5 0.714 (0.018) 6.0 (0.6) 11.2 (1.1) 41.9 (2.0) 2PYO 0.712 (0.019) 5.9 (0.6) 11.2 (1.1) 41.9 (2.1) Discussion Nucleosomal DNA is B-like at the dinucleotide step level An analysis of the twenty-nine nucleosome X-ray crystal structures of better than 3 Å resolution reveals significant dinucleotide level structural variability in nucleosomal DNA, despite limited variation in sequence, with only six unique sequences, of which only one differs significantly from the other five.

As a result of variation in kinks versus smooth bending, the variation in the shift parameter is also not uniformly different for the regions binding H3 and H4 as against the regions binding H2A and H2B, as noted for 1KX5   [ 17 ].

Studies of the best resolved nucleosome structure (PDB id: 1KX5 , [ 15 ]) have shown that the parameter roll is primarily responsible for curvature of the nucleosome [ 17 ], while twist and slide contribute predominantly to the pitch of the nucleosome [ 17 - 19 ].

Crosscorrelation values for the successive bending angles, and the minor groove width, for the five structures with PDB id's 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 and 5, with respect to the corresponding parameters for the best resolved crystal structrure of the nucleosome with PDB id 1KX5 , corresponding to sequence 6.

We observe at least one kinked GG/CC step in all structures with the exception of 1KX5 , 1M18 , 1M19 , 1M1A , 2CV5 and 2PYO .

These results also raise questions about the rationale for using only the best resolved X-ray crystal structure (PDB id: 1KX5 , [ 15 ]) of nucleosome as the prototype on which different potential nucleosome sequences are threaded, for calculating the energetic cost of nucleosome formation [ 18 , 20 - 22 ].

The trajectories for the dinucleotide step parameters, for the six structures, namely, 1KX4 , 2NZD , 2F8N , 1KX3 , 1P3I and 1KX5 , corresponding to sequences 1, 2, 3, 4, 5 and 6 respectively, are shown in figures S1-S6 of additional file 1 .

Figure S9 in additional file 1 shows the trajectories for the successive bending angles for the six representative structures, while Figure 5 (upper panel) shows the crosscorrelation values for the successive bending angles, for the five structures 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , with respect to the corresponding parameters for the structrure 1KX5 .

The best resolved nucleosome crystal structure may not be the 'ideal' template Several studies have focussed on developing algorithms to predict the energetic cost of nucleosome formation [ 18 , 20 - 22 ] by using as a template, the best resolved X-ray crystal structure of nucleosome with PDB id 1KX5   [ 15 ].

This has been discussed by Richmond and Davey [ 17 ] for the structure 1KX5 .

We see major drawbacks in this approach, since our analysis clearly points at significant variation in local nucleosomal structure, and hence it seems unlikely that the single static structure represented in 1KX5 is the structure for nucleosomal DNA.

Sequences 1 and 2 had only one corresponding structure, namely 1KX4   [ 15 ] and 2NZD [ 31 ] respectively, sequences 3 and 6 had two corresponding structures, namely 1U35   [ 49 ] and 2F8N   [ 31 ], and 1KX5   [ 15 ] and 2PYO   [ 50 ] respectively, sequence 4 had three corresponding structures, namely 1AOI   [ 51 ], 1KX3   [ 15 ] and 2CV5   [ 27 ], while the remaining twenty structures ( 1EQZ   [ 52 ], 1F66   [ 53 ], 1M18 , 1M19 , 1M1A   [ 54 ], 1P34 , 1P3A , 1P3B , 1P3F , 1P3G , 1P3I , 1P3K , 1P3L , 1P3M , 1P3O , 1P3P   [ 55 ], 1S32   [ 56 ], 1ZLA   [ 57 ], 2NQB   [ 31 ], 3C1B   [ 58 ]) correspond to sequence 5.

Crosscorrelation values for the rotational parameters roll and twist, and the translational parameter slide, for the five structures with PDB ids 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 and 5, with respect to the corresponding parameters for the best resolved crystal structrure of the nucleosome with PDB id 1KX5 , corresponding to sequence 6.

It was shown by Richmond and Davey [ 17 ] in the structure 1KX5 that the regions between SHL -3 and SHL +3 display smooth bending when the minor groove faces the histone octamer while the minor groove blocks facing the histone octamer and farther away from the dyad are kinked with large negative roll angle values.

Given that DNA curvature is essentially statistical [ 42 - 44 ], and considering that statistical and static averages are often different [ 45 , 46 ], the structure 1KX5 is unlikely to represent the statistical mean of such an ensemble.

It must be noted here that the 'Complex' dataset analysed by Marathe et al. also included two representative nucleosome structures 1KX5 and 1KX3 .

Hence calculation of the energetic cost for a given genomic sequence to take up a nucleosome structure, assuming the structure of 1KX5 as the template, may not lead to biologically meaningful results.

Figure 4 shows the crosscorrelation values for the parameters roll, twist and slide, for the five structures 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 and 5, with respect to the parameters for the best resolved crystal structrure 1KX5 , corresponding to sequence 6.

The largest number (26) of kinks are observed in the structure 1U35 , while the smallest number (6) of kinks are observed in the structure 1KX5 .

Crosscorrelation values for the angles between global helix axes fitted to backbone C 1 ' atoms of successive, non-overlapping tetranucleotide fragments, and the angles between global helix axes fitted to backbone C 1 ' atoms of successive, non-overlapping pentanucleotide fragments, for the five structures with PDB id's 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 and 5, with respect to the corresponding parameters for the best resolved crystal structrure of the nucleosome with PDB id 1KX5 , corresponding to sequence 6.

It must be noted that the structure 1KX5 also has a sharp kink at +2.

All the structures corresponding to sequences 1 (PDB id 1KX4 ), 2 (PDB id 2NZD ), 4 (PDB id's 1AOI , 1KX3 and 2CV5 ) and 6 (PDB id's 1KX5 and 2PYO ), as well as one structure corresponding to sequence 3 (PDB id 2F8N ) and two structures corresponding to sequence 5 (PDB id's 1EQZ and 2NQB ) comprise of wild-type histones, though the histone sequence might vary at a few amino acid positions depending on the organism from which it was derived.

Publication Year: 2011


The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation.

(2011) Mol Cell 41

PubMed: 21329878 | PubMedCentral: PMC3093613 | DOI: 10.1016/j.molcel.2011.01.025

Figure 3 Extraction of Long-Range Distances between Spin-Labeled H3-H4 Dimers Agrees with a Tetrameric Conformation When Bound to Nap1 (A) Positions of spin labels on H4 R45 and H3 Q12... (green spheres) are shown on the structure of the tetramer taken from the nucleosome (PDB code 1KX5, images created with Pymol, http://www.pymol.org/ ).

Publication Year: 2011


Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes.

(2011) Nat Commun 2

PubMed: 21587230 | PubMedCentral: PMC3112535 | DOI: 10.1038/ncomms1320

( c – e ) Comparison of experimental scattering profiles (black) with a scattering profile calculated using FoXS 51 from the Xl-nucleosome crystal structure (1kx5; red).

The scattering curve calculated from the crystal structure (1kx5; ref.

Publication Year: 2011


On the structure and dynamics of the complex of the nucleosome and the linker histone.

(2011) Nucleic Acids Res 39

PubMed: 21355036 | PubMedCentral: PMC3130272 | DOI: 10.1093/nar/gkr101

MATERIALS AND METHODS Structure preparation The crystal structure of the nucleosome core particle ( 15 ) (NCP, Protein Data Bank—PDB code 1kx5, 1.9 Å resolution) was used as a ... eference structure.

Publication Year: 2011


Histone variant innovation in a rapidly evolving chordate lineage.

(2011) BMC Evol Biol 11

PubMed: 21756361 | PubMedCentral: PMC3156773 | DOI: 10.1186/1471-2148-11-208

Amino acid substitutions were evaluated using 3D-structure predictions for Oikopleura histone variants obtained from I-tasser [ 82 ] with the crystal structure of the Xenopus nucleosome specified as a... template (PDB file 1kx5:A for histone H3, 1kx5:B for histone H4, 1kx5:C for histone H2A and 1kx5:D for histone H2B).

PDB files of Oikopleura histone variants were viewed and aligned to PDB files of nucleosome crystal structures (PDB files 1kx5 and 1f66) in Pymol (Version 1.2r3pre, Schrödinger, LLC).

Publication Year: 2011


Structure of RCC1 chromatin factor bound to the nucleosome core particle.

(2010) Nature 467

PubMed: 20739938 | PubMedCentral: PMC3168546 | DOI: 10.1038/nature09321

(d) Histone H4-histone crystal contacts in nucleosome core particle (NCP) crystal structure (PDB id 1KX5).

The structure was solved by molecular replacement using Phaser software 39 and a search model containing three rigid bodies: Drosophila RCC1(39–211, 242–415), the histone octamer with histone tails removed, and the 147 bp human α-satellite DNA (PDB id 1KX5) with the DNA bases manually changed to match the Widom 601 sequence (Phaser final log-likelihood gain of 7292).

Publication Year: 2010


Statistical investigation of position-specific deformation pattern of nucleosome DNA based on multiple conformational properties.

(2011) Bioinformation 7

PubMed: 22125381 | PubMedCentral: PMC3218313 | DOI: null

Methodology Structural data of NCPs The experimental database is constructed by collecting 6870 base pair steps from 48 nucleosome crystal structures in the Protein Data Bank (PDB), including 1AOI, 1E... Z, 1F66, 1ID3, 1KX5, 1KX4, 1KX3, 1M1A, 1M19, 1M18, 1P3P, 1P3O, 1P3M, 1P3L, 1P3K, 1P3I, 1P3G, 1P3F, 1P3B, 1P3A, 1P34, 1S32, 2CV5, 1U35, 1ZLA, 2F8N, 2FJ7, 2NZD, 2NQB, 2PYO, 3B6G, 3B6F, 3C1C, 3C1B, 3KUY, 3LJA, 3KWQ, 3LEL, 3AFA, 3A6N, 3MGS, 3MGR, 3MGQ, 3MGP, 3KXB, 3MVD, 3LZ0 and 3LZ1.

Publication Year: 2011


Role of histone tails in structural stability of the nucleosome.

(2011) PLoS Comput Biol 7

PubMed: 22207822 | PubMedCentral: PMC3240580 | DOI: 10.1371/journal.pcbi.1002279

The dihedral angles (O3'-P-O5'-C5'), (P-O5'-C5'-C4'), (O5'-C5'-C4'-C3'), (C5'-C4'-C3'-O3'), (C4'-C3'-O3'-P) and (C3'-O3'-P-O5') obtained from the intact nucleosome simulation are compared with those f... om the crystal structure (1KX5.

In the crystal structure of the nucleosome core particle (1KX5.

g001 Figure 1 Architecture of the nucleosome core particle (PDB ID 1KX5; [ 2 ] ).

Molecular Dynamics Simulation Set-up The starting structure of all molecular dynamics (MD) simulations was taken from the Å resolution crystal structure of the nucleosome core particle (PDB ID: 1KX5) [2] .

Publication Year: 2011


From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: nanoscale modeling of the nucleosomal stem.

(2011) Nucleic Acids Res 39

PubMed: 21835779 | PubMedCentral: PMC3241633 | DOI: 10.1093/nar/gkr573

The rigid part is the central part of the core DNA in the crystal structure (PDB ID 1kx5).

Publication Year: 2011


Structural basis of Ets1 cooperative binding to widely separated sites on promoter DNA.

(2012) PLoS One 7

PubMed: 22432043 | PubMedCentral: PMC3303851 | DOI: 10.1371/journal.pone.0033698

( A ) Docking of Ets1 homodimer to nucleosomal DNA based on the superimposition of DNA in the (Ets1) 2 •2DNA structure and the high-resolution structure of a nucleosome core particle (PDB acce... s code 1kx5) [49] .

Publication Year: 2012


Micrococcal nuclease does not substantially bias nucleosome mapping.

(2012) J Mol Biol 417

PubMed: 22310051 | PubMedCentral: PMC3314939 | DOI: 10.1016/j.jmb.2012.01.043

For reference, the core particle structure 21 (PDB ID: 1KX5 ), viewed along the nucleosomal dyad axis, is also shown (c).

Publication Year: 2012


Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.

(2012) J Chem Theory Comput 8

PubMed: 22582031 | PubMedCentral: PMC3348677 | DOI: 10.1021/ct200909j

The systems used consisted of partially folded TRPCage 52 (304 atoms), ubiquitin 53 , 54 (1231 atoms, PDB code 1UBQ ), apo-myoglobin (2492 atoms), and nucleosome (25 095 atoms, PDB code 1KX5 )...

Publication Year: 2012


Mg2+ in the major groove modulates B-DNA structure and dynamics.

(2012) PLoS One 7

PubMed: 22844516 | PubMedCentral: PMC3402463 | DOI: 10.1371/journal.pone.0041704

In the best resolved NCP structure (PDB code 1KX5), 12 Mn 2+ (mimicking Mg 2+ ) are observed in the DNA major groove [50] , [51] .

Publication Year: 2012


The conformational flexibility of the C-terminus of histone H4 promotes histone octamer and nucleosome stability and yeast viability.

(2012) Epigenetics Chromatin 5

PubMed: 22541333 | PubMedCentral: PMC3439350 | DOI: 10.1186/1756-8935-5-5

(B) Ribbon diagram showing the histone H3/H4 heterotetramer from the nucleosome core particle (PDB:1KX5) [ 26 ] oriented so that the H3/H4 dimer on the left is superimposed with the H3/H4 dimer in (A)...

Publication Year: 2012


Crystal structure of a plectonemic RNA supercoil.

(2012) Nat Commun 3

PubMed: 22692544 | PubMedCentral: PMC3518024 | DOI: 10.1038/ncomms1903

Figure 3 Schematic illustrations of nucleic-acid superstructures Shown are 1.5 or 2.0 turns of coiled coils, color coded by individual strands, for crystal structures of ( a ) supercoiled RNA (this wo... k), ( b ) coiled-coiled DNA (PDB accession code 2AF1) 11 , and ( c ) nucleosome core particle DNA (PDB accession code 1KX5) 16 .

In contrast, the continuous, nonuniform bending of the DNA superhelix in the structure of the nucleosome core particle (PDB accession code 1KX5) 16 reveals significant deviations in both major (8.9 – 15.6 Å) and minor (2.5 – 9.4 Å) groove widths ( Fig. 3f ); the 2.5-Å minor groove width is induced by the insertion of histone-arginine side-chains at several minor groove positions within the nucleosome DNA.

34 ) for the 147-bp nucleosome core particle DNA structure at 1.9-Å resolution (PDB entry 1KX5) 16 .

Publication Year: 2012


Easy DNA modeling and more with GraphiteLifeExplorer.

(2013) PLoS One 8

PubMed: 23308263 | PubMedCentral: PMC3538550 | DOI: 10.1371/journal.pone.0053609

Missing DNA between two nucleosomal complexes containing DNA (PDB code 1KX5) is modeled with GraphiteLifeExplorer (upper image).

Publication Year: 2013


An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions.

(2013) PLoS One 8

PubMed: 23418426 | PubMedCentral: PMC3572162 | DOI: 10.1371/journal.pone.0054228

The root mean square deviation (RMSD) values between the HO structure and the initial HO model generated from the 1KX5 crystal structure have been monitored during the course of the simulations.

Supporting Information Figure S1 RMSD of the histone octamer compared to its starting configuration generated from the 1KX5 crystal structure, observed during the course of the simulation for a system with a single NCP and K + counterions (1NCP/K + ).

The initial coordinates of the beads (of total number 710) were set to the centres of mass of the amino acids determined from the NCP high resolution crystal structure (entry code 1KX5.

( B ) The nucleosome crystal structure at 1.9 Å resolution (pdb 1KX5 [2] ).

The histone tails were modelled as 10 strings of linearly-connected beads of the length and amino acid sequence according to the PDB entry 1KX5.

Publication Year: 2013


Quantitating the specificity and selectivity of Gcn5-mediated acetylation of histone H3.

(2013) PLoS One 8

PubMed: 23437046 | PubMedCentral: PMC3578832 | DOI: 10.1371/journal.pone.0054896

g002 Figure 2 Structure of H3 (blue highlight) in nucleosome, which is constructed from the PDB 1KX5 nucleosome structure [54] .

Publication Year: 2013


Reconstitution of hemisomes on budding yeast centromeric DNA.

(2013) Nucleic Acids Res 41

PubMed: 23620291 | PubMedCentral: PMC3675498 | DOI: 10.1093/nar/gkt314

( A ) Structural model based on PDB 1KX5, showing that a 62-bp duplex is sufficient to wrap a hemisome.

Publication Year: 2013


The octamer is the major form of CENP-A nucleosomes at human centromeres.

(2013) Nat Struct Mol Biol 20

PubMed: 23644596 | PubMedCentral: PMC3760417 | DOI: 10.1038/nsmb.2562

Molecular Modeling Molecular models were generated using PDB ID 1KX5 and 1ZBB for the H3-containing particles and 3AN2 for CENP-A-containing particles.

Publication Year: 2013


DBSI: DNA-binding site identifier.

(2013) Nucleic Acids Res 41

PubMed: 23873960 | PubMedCentral: PMC3763564 | DOI: 10.1093/nar/gkt617

The basic residue-level electrostatics feature is mapped onto the surface of the Nucleosome Core Particle (PDB 1KX5).

Publication Year: 2013


Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3?, MSK1, and MKP1.

(2013) Bioinform Biol Insights 7

PubMed: 24027420 | PubMedCentral: PMC3767654 | DOI: 10.4137/BBI.S12449

Molecular association of native MKP1 with histone H3 and its PTM modified structure The full length (1–21 aa) loop structure of histone H3 from the crystal structure of the Xenopus nucleosome ... PDB ID: 1KX5) was used.

Figure S3 Full-length loop structure of histone H3 peptide from PDB: 1KX5 was modified by phosphorylation of Ser10 and acetylation of Lys9 and Lys14.

Publication Year: 2013


Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal.

(2013) PLoS One 8

PubMed: 24265699 | PubMedCentral: PMC3827064 | DOI: 10.1371/journal.pone.0078587

Results SAXS data were taken on all nucleosomes and the scattering data were compared to theoretical scattering predictions from CRYSOL on the 1kx5 crystal structure [ 7 ] (modified to remove tails wh... re appropriate).

The 1kx5 structure was first modified to have either extended or folded tails.

Publication Year: 2013


Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.

(2013) PLoS Comput Biol 9

PubMed: 24278005 | PubMedCentral: PMC3836855 | DOI: 10.1371/journal.pcbi.1003354

Methods Molecular dynamics simulations and free energy calculations of fully solvated and neutralized mono-nucleosomes were carried on the X-ray structure with PDB code 1KX5 [34] .

Publication Year: 2013


Automethylation activities within the mixed lineage leukemia-1 (MLL1) core complex reveal evidence supporting a "two-active site" model for multiple histone H3 lysine 4 methylation.

(2014) J Biol Chem 289

PubMed: 24235145 | PubMedCentral: PMC3887211 | DOI: 10.1074/jbc.M113.501064

A, surface representation of the nucleosome core particle (PDB code 1KX5 ( 61 )) is shown with the position of H3K4 indicated.

Publication Year: 2014


A CENP-S/X complex assembles at the centromere in S and G2 phases of the human cell cycle.

(2014) Open Biol 4

PubMed: 24522885 | PubMedCentral: PMC3938055 | DOI: 10.1098/rsob.130229

Top: top view of the nucleosomal structure including DNA (1kx5, [ 49 ]) with both H3 molecules coloured in red and blue, respectively; the H3 C-termini are indicated by coloured spheres.

Publication Year: 2014


Nucleosomes accelerate transcription factor dissociation.

(2014) Nucleic Acids Res 42

PubMed: 24353316 | PubMedCentral: PMC3950707 | DOI: 10.1093/nar/gkt1319

(E) Structure of the nucleosome (PDB: 1KX5) that indicates the location of the TF-target sequence (red), the Cy3 fluorophore location (green) and the Cy5 fluorophore location (magenta).

Publication Year: 2014


Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription.

(2014) Elife 3

PubMed: 24668167 | PubMedCentral: PMC3965291 | DOI: 10.7554/eLife.01632

3D modeling The acetylation of H3K64 was modelled on the 1KX5 Xenopus laevis nucleosome core particle structure ( Davey and Richmond, 2002 ).

( A ) Distances in Å between DNA backbone phosphate oxygen atoms and H3K64 main-chain amide (red text) or terminal nitrogen atoms (black text) in the high-resolution (1.9 Å) crystal structure of the nucleosome (PDB ID 1KX5).

( C ) The side-chain of H3K64 is part of an extensive water-mediated hydrogen bonding network between histones and DNA in the high-resolution crystal structure of the nucleosome (PDB ID 1KX5).

Interestingly, in the high-resolution crystal structure of the nucleosome (PDB 1KX5; Davey et al., 2002 ) H3K64 is found to be involved in an extensive network of water-mediated hydrogen bonds that link numerous water molecules, histone side- and main-chain atoms and the DNA ( Figure 5—figure supplement 5C ).

Publication Year: 2014


Binding of PHF1 Tudor to H3K36me3 enhances nucleosome accessibility.

(2013) Nat Commun 4

PubMed: 24352064 | PubMedCentral: PMC4007151 | DOI: 10.1038/ncomms3969

(c) Crystal structure of the NCP (PDB ID: 1KX5) that indicates the positions of H3 (orange); MLA at H3K36C (dark red); Cy5 at H2AK119C (purple); Cy3 at the 5 prime end of 601L (green); and the LexA ta... get site (cyan).

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4017609

(A) Complete NCP structure from PDB: 1KX5.

Publication Year: 2014


Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.

(2014) Nucleic Acids Res 42

PubMed: 24829460 | PubMedCentral: PMC4066768 | DOI: 10.1093/nar/gku338

To obtain insight into the A-tract behaviour in the nucleosome, we performed threading of the tracts through a high-resolution nucleosome crystal structure (1kx5 ( 90 )).

Publication Year: 2014


Nucleosomes shape DNA polymorphism and divergence.

(2014) PLoS Genet 10

PubMed: 24991813 | PubMedCentral: PMC4081404 | DOI: 10.1371/journal.pgen.1004457

Structural mapping of divergence rates To elucidate the distribution of the smoothed (as above) divergence on DNA from the structure of the nucleosome we colored-coded values of each base pair in a sc... ematic rendering of the DNA strands of pdb1kx5 [55] using PyMOL [89] .

Publication Year: 2014


Thymoquinone-induced conformational changes of PAK1 interrupt prosurvival MEK-ERK signaling in colorectal cancer.

(2014) Mol Cancer 13

PubMed: 25174975 | PubMedCentral: PMC4158125 | DOI: 10.1186/1476-4598-13-201

A. Model of IPA-3 bound autoinhibited dimer conformation of PAK1 (PDB id:1kx5).

Publication Year: 2014


Synergistic modulation of cyclobutane pyrimidine dimer photoproduct formation and deamination at a TmCG site over a full helical DNA turn in a nucleosome core particle.

(2014) Nucleic Acids Res 42

PubMed: 25389265 | PubMedCentral: PMC4245940 | DOI: 10.1093/nar/gku1049

Orientations were approximated from the crystal structure of a nucleosome core particle 1KX5.

Replacement of the base pairs corresponding to positions 1–10 in the high resolution (1.9 Å) crystal structure of a 147-mer nucleosome core particle 1KX5.

Publication Year: 2014


Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure??a FRET study.

(2015) Nucleic Acids Res 43

PubMed: 25589544 | PubMedCentral: PMC4330349 | DOI: 10.1093/nar/gku1354

Bulk and spFRET experiments on mononucleosomes: ( A ) crystal structure (pdb file 1kx5, with hypothetical DNA extension taken from pdb file 1bna) and approximate dye positions for end-labeled nucleoso... es (dl-E), internally labeled nucleosomes (dl-I) and protein–DNA labeled nucleosomes (H2B-int) that are formed in dimer exchange experimenys.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4330383

Structure determination and refinement The structure of H3-H4-MCM2 (69–138) complex was determined by molecular replacement using MOLREP ( 43 ) with the H3-H4 histones structure (chain A and B... of PDB entry 1KX5) as model probe.

Correctness of the solution was confirmed by the superposition of the full H3-H4 tetramer (chains A, B, E and F of PDB entry 1KX5) by applying the R 32 2-fold crystallographic symmetry.

(A) Ribbon representation of the MCM2 69 – 121 −H3 23 – 100 −H4 57 – 134 complex compared to the structure of the nucleosome (PDB code 1KX5 ( 1 )) on the left and right panels, respectively.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4365049

DNA structures at both ends of nucleosomal DNA (13 bp at each end) were missing from the CENP-A nucleosome, but they were modeled based on the DNA structure of the canonical H3 nucleosome by structura... ly aligning the phosphate atoms of backbones (residue numbers, from −60 to 60) of 3an2 with those of 1kx5 to ensure that the length of DNA was equal for all systems.

The simulations were performed with two crystal structures, i.e., the canonical H3 nucleosome (PDB code: 1kx5)[ 7 ] and the CENP-A nucleosome (PDB code: 3an2) [ 3 ] and two structures in which the nucleosomal DNA sequences were exchanged to determine whether DNA sequence dependency occurred, although both DNAs were α-satellite derivatives.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4402545

For example, the average C1′–C1′ distance in the curved nucleosome structure (PDBID: 1KX5) is ∼10.6 Å ± 0.3 Å.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4434184

A constant ω = 34.8°, average twist for the 1kx5 X-ray crystal structure of nucleosome-bound DNA, was used for all dinucleotide steps.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4446432

The N-tails of all histones within the nucleosome core particle (pdb: 1KX5; MacPyMOL) are represented in the ‘spheres’ configuration.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4446439

The molecule shown contains the histone octamer from the 1.9 Å structure of the nucleosome core particle to show the extent of the histone tails (PDB code 1KX5), the DNA from the 2.5 Å... structure of the 601 nucleosome core particle to show the 145 bp nucleosomal DNA (PDB code 3LZ0), and 31 bp of modeled B-form extranucleosomal DNA.

The results are mapped on the space filling representation of the 1.9 Å crystal structure of the nucleosome core particle (PDB code 1KX5).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4532510

Nucleosome The nucleosome we simulated is the same molecular complex as the X-ray crystal structure with the pdb code 1KX5 [ 2 , 4 ] ( Fig 1 ).

g001 Fig 1 X-ray crystal structure of nucleosome (pdb code 1KX5.

Publication Year: 2015