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PDB ID Mentions in PubMed Central Article count: 9

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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

Mn 2+ binding sites are indicated above the base sequence by the yellow and light blue arrows (solid, binding the DNA major groove; broken, binding the DNA minor groove) in the structures of human and... X.laevis NCPs (PDB code 1KX3) ( 11 ), respectively.

The histone octameric structures of human NCP and other NCPs [2.0 Å resolution structure of Xla -NCP (PDB code 1KX3) ( 11 ), yeast NCP (PDB code 1ID3) ( 14 ) and chicken NCP (PDB code 1EQZ) ( 13 )] were compared by superimposing residues (H3: 38–134, H3′: 38–135, H4: 25–102, H4′: 18–102, H2A: 14–118, H2A′: 15–118, H2B: 32–125, H2B′: 31–124) in each human histone subunit onto their equivalents from other species; thus, an overall root-mean-square deviation (r.m.s.d.) was estimated to be as small as 1.3 Å (1.30, 1.29 and 1.41 Å for the above NCPs, respectively).

The differences in helical twist are shown by the superposition between human (yellow) and X.laevis (light blue; PDB code 1KX3) ( 11 ) NCPs, based on the histone octamers alone.

The best superposition between human (yellow) and X.laevis (light blue; PDB code 1KX3) ( 11 ) NCPs, based on the histone octamers alone, reveals the discrepancy in the DNA structures.

( B – D ) The close-up stereo views of the boxed area in (A) show the discrepancy in the DNA structures by the superposition between human (yellow) and X.laevis (light blue; PDB code 1KX3) ( 11 ) NCPs, based on the histone octamers alone.

This value is substantially larger than those of other NCP structures, such as 2.55 Å for Xla -NCP (PDB code 1KX3) ( 11 ), 2.44 for yeast NCP (PDB code 1ID3) ( 14 ) and 2.67 for chicken NCP (PDB code 1EQZ) ( 13 ), demonstrating that the human nucleosomal DNA takes a different path.

Of these sites, six at the base pair locations of −60, −47, 3, 35, 48 and 61 were the same binding sites ( Figure 2A ) as those in the 2.0 Å structure of Xla -NCP (PDB code 1KX3) ( 11 ).

Publication Year: 2005


Sequence-dependent DNA deformability studied using molecular dynamics simulations.

(2007) Nucleic Acids Res 35

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

( a ) Nucleosome core structure ( 31 ) (PDB: 1kx3) drawn using Pymol software ( 50 ).

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.

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 core structures.

Publication Year: 2007


DNA conformations and their sequence preferences.

(2008) Nucleic Acids Res 36

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

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, ... zey, 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


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

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 stru... ture (1AOI [ 89 ]) is calculated as 41.5 Å, indicating that the DNA in different nucleosome structures has small variations in curvature.

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.

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

1EQZ and 1KX3 structures are quasi identical (RMSD ∼0.8 Å); the significance of the 2CV5 DNA fine structure appeared problematic, due to tight DNA–DNA contacts within the cryst... l that notably altered the DNA conformation ( 61 ).

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


Integration of open access literature into the RCSB Protein Data Bank using BioLit.

(2010) BMC Bioinformatics 11

PubMed: 20429930 | PubMedCentral: PMC2880030 | DOI: 10.1186/1471-2105-11-220

Related Citations in PDB entry as provided by the depositors of the structure; PubMed Central articles are articles identified by BioLit that mention the PDB ID; Other PDB IDs (not shown) that co-occu... with 1KX3 in PubMedCentral articles.

Figure 1 Literature tab view for PDB ID 1KX3 from the RCSB PDB .

Publication Year: 2010


ICM Web: the interactive chromatin modeling web server.

(2010) Nucleic Acids Res 38

PubMed: 20542915 | PubMedCentral: PMC2896153 | DOI: 10.1093/nar/gkq496

The corresponding results for pdb entry 1kx3 are 173 kcal/mol-nuc ∼ 2.0 k b T/bps and 502 kcal/mol-nuc ∼ 5.8 k b T/bps (1kx3 has 146 instead of ... 47 bp).

Publication Year: 2010


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

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 show... 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 .

For example, while the GG/CC step at location -1.5 in the structure 1KX3 assumes tilt, roll, twist, shift, slide and rise values of 7.5°, -26.1°, 43.3°, -0.4 Å, 0.4 Å and 4.0 Å respectively, the neighbouring GC/GC step assumes values of -15.5°, -17.0°, 37.3°, 0.6 Å, 0.5 Å and 4.6 Å respectively.

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

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.

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.

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.

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 , corresponding 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.

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.

Publication Year: 2011


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