Citations in PubMed

Primary Citation PubMed: 9305837 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 33

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

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

Molecular replacement, with the PDB entry 1AOI ( 12 ) as the search model, was used to obtain the initial phases via Amore ( 27 ).

The crystal structure was determined by the molecular replacement method, using the previously published Xla -NCP structure (PDB entry 1AOI) ( 12 ) as a search model.

Publication Year: 2005


Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.

(2006) Nucleic Acids Res 34

PubMed: 16528101 | PubMedCentral: PMC1401507 | DOI: 10.1093/nar/gkl009

Modelled DNA is shown as a grey surface and based on existing crystal structures of wrapped DNA (PDB code 1AOI) ( 57 ) and electron microscopy studies of LrpC ( 27 ).

Publication Year: 2006


The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure.

(2006) Nucleic Acids Res 34

PubMed: 16714444 | PubMedCentral: PMC1464108 | DOI: 10.1093/nar/gkl338

( C ) Surface modifications are modeled on the crystal structure of the nucleosome (pdb file 1AOI) ( 10 ).

Publication Year: 2006


Insights into protein-DNA interactions through structure network analysis.

(2008) PLoS Comput Biol 4

PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170

Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).

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.

Publication Year: 2009


Polycomb group genes: keeping stem cell activity in balance.

(2008) PLoS Biol 6

PubMed: 18447587 | PubMedCentral: PMC2689701 | DOI: 10.1371/journal.pbio.0060113

Table 1 Mouse PcG Knockout Phenotype Figure 1 Nucleosome Crystal Structure and Potential Effect of Mono-Ubiquinated H2A on Chromatin Accessibility (A) Representation of the nucleosome crystal structur... at 2.8 Å resolution (Protein Data Bank #1AOI) [ 31 ].

Publication Year: 2008


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

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.

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

Publication Year: 2009


Super-coil me: sizing up centromeric nucleosomes.

(2009) J Cell Biol 186

PubMed: 19704018 | PubMedCentral: PMC2733755 | DOI: 10.1083/jcb.200908012

(Structural representations were created using Chimera and PDBID: 1aoi ( 1 ).

The transparent image shown was adapted from the RCSB's PDB Molecule of the Month by David Goodsell using PDBID: 1aoi ( 1 ) doi: 10.2210/rcsb_pdb/mom_2000_7 .

Publication Year: 2009


Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II.

(2009) Nat Struct Mol Biol 16

PubMed: 19935686 | PubMedCentral: PMC2919570 | DOI: 10.1038/nsmb.1689

To evaluate the possibility of Ø-loop formation by Pol II, we modeled the Ø-loop by docking the high-resolution structures of yeast Pol II EC onto the nucleosome (PDB IDs 1aoi and 1y1w... see refs.

The structures of a nucleosome and yeast Pol II EC (PDB IDs 1aoi and 1y1w, see refs.

Publication Year: 2009


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

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.... ) 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.

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.

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.

Publication Year: 2011


PubMed ID is not available.

Published in 2011

PubMedCentral: PMC3061088

In the figure, this structural feature of the nucleosome-nucleosome stacking interface is illustrated using the 1AOI nucleosome core particle crystal structure (top).

Publication Year: 2011


Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes.

(2011) Nucleic Acids Res 39

PubMed: 21278419 | PubMedCentral: PMC3105411 | DOI: 10.1093/nar/gkr005

( A ) The crystal structure of the nucleosome core particle [PDB entry 1AOI, ( 22 )], which consists of two copies each of H2A (yellow), H2B (red), H3 (blue), H4 (green) and 147 bp of DNA (gra... ), with the histone tails removed, serves as a reference.

( C ) (Left panel) Experimental scattering data (red) superimposed with simulated data from the crystal structure (black), generated with the program CRYSOL ( 41 ) with PDB entry 1AOI as input (histone tails removed from the model).

The experimental scattering data and the P(r) functions for this particle superimpose very well with scattering data simulated from the nucleosome crystal structure (pdb entry 1AOI, flexible histone tails removed; Figure 5 C) using the program CRYSOL ( 41 ).

( B.2 ) Experimental scattering data for W-Nuc165 (red), simulated data from the crystal structure 1AOI (histone tails removed, black) and simulated data from a model for W-Nuc165 (blue) are superimposed.

Publication Year: 2011


Bridging the resolution gap in structural modeling of 3D genome organization.

(2011) PLoS Comput Biol 7

PubMed: 21779160 | PubMedCentral: PMC3136432 | DOI: 10.1371/journal.pcbi.1002125

The DNA then wraps around histone proteins forming nucleosomes ([C], the complex between nucleosome core particles and DNA from PDB entry 1AOI [49] ).

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


Characterization of chromoshadow domain-mediated binding of heterochromatin protein 1? (HP1?) to histone H3.

(2012) J Biol Chem 287

PubMed: 22493481 | PubMedCentral: PMC3365711 | DOI: 10.1074/jbc.M111.337204

A , space-filling representation of the H3 residues that are significantly shifted ( yellow ) or “quenched” ( red ) on addition of CSDα, mapped onto the nucleosome (Protein Dat... Bank code 1AOI ( 30 )).

Publication Year: 2012


The role of epigenetic mechanisms and processes in autoimmune disorders.

(2012) Biologics 6

PubMed: 23055689 | PubMedCentral: PMC3459549 | DOI: 10.2147/BTT.S24067

Luger K Mäder AW Richmond RK Sargent DF Richmond TJ Crystal structure of the nucleosome core particle at 2.8 A resolution Nature 1997 389 6648 251 260 9305837 Figure 1 ( A ) Cartoon derived fr... m the crystal structure (Protein Data Bank iD: 1aoi 298 ) of the histone octamer (H2A, blue; H2B, purple; H3, green; H4, orange) surrounded by 1.65 turns of DNA (∼147 base pair fragment).

Publication Year: 2012


Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

(2012) BMC Bioinformatics 13

PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165

Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH &#... 000a0;     Cro & repressor 1LMB   Homeodomain 1FJL, 1HDD, 6PAX   LacI repressor 1WET   Endonuclease Fok1 1FOK   Gamma Delta resolvase 1GDT   Hin recombinase 1HCR   RAP1 family 1IGN   Prd paired domain 1PDN   Tc3 transposase 1TC3   Trp repressor 1TRR   Diptheria tox repressor 1DDN   Transcription factor IIB 1D3U   Interferon regulatory 2IRF   Catabolite gene activator protein 1RUO   Transcription factor 1CF7, 3HTS   Ets domain 1BC8 Zinc Co-ordinating       β-β-α zinc finger 1ZAA   Harmone Nuclear Receptor 2NLL   Loop sheet helix 1TSR   GAL4 type 1ZME Zipper type       Leucine Zipper 1YSA   Helix loop helix 1AN2 Other-α Helix       Pappilomavirus 1 E2 2BOP   Histone 1AOI   EBNA1 nuclear protein 1B3T   Skn-1 transcription factor 1SKN   Cre Recombinase 1CRX   High Mobility Group 1QRV   MADS box 1MNM β-Sheet       TATA box binding 1YTB β-Hairpin/Ribbon       MetJ repressor 1CMA   Tus replication terminator 1ECR   Integration host factor 1IHF   Transcription Factor T-domain 1XBR   Hyperthermophile DNA 1AZP   Arc repressor 1PAR Other       ReI homology 1SVC   Stat protein 1BF5 Enzyme       Methyltransferase 6MHT   Endonuclease PvuII 3PVI   Endonuclease ecorV 1RVA   Endonuclease ecorI 1QPS   Endonuclease BamHI 3BAM   Enonuclease V 1VAS   Dnase I 2DNJ   DNA mismatch endonuclease 1CW0   DNA polymerase β 1BPY   DNA Polymerase I 2BDP   DNA Polymerase T7 1T7P,1CLQ   HIV Reverse Transcriptase 2HMI   Uracil DNA glycosylase 1SSP   3-Methyladenine DNA glycosylase 1BNK   Homing endonuclease 1A73, 1BP7   TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).

Publication Year: 2012


Histone H2A variants in nucleosomes and chromatin: more or less stable?

(2012) Nucleic Acids Res 40

PubMed: 23002134 | PubMedCentral: PMC3510494 | DOI: 10.1093/nar/gks865

( B ) Nucleosome crystal structure based on [( 8 ), PDB ID: 1AOI].

Publication Year: 2012


Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes.

(2013) Nucleic Acids Res 41

PubMed: 23396443 | PubMedCentral: PMC3616739 | DOI: 10.1093/nar/gkt074

Molecular modelling of the LEDGF PWWP binding to the MN The solution NMR structure of LEDGF PWWP was docked onto the crystal structure of nucleosome core particle (PDB # 1AOI) ( 40 ).

Publication Year: 2013


The structure of the FANCM-MHF complex reveals physical features for functional assembly.

(2012) Nat Commun 3

PubMed: 22510687 | PubMedCentral: PMC3646547 | DOI: 10.1038/ncomms1779

Calculated electrostatic on the surface of (MHF1-MHF2) 2 tetramer ( a ) and (H3-H4) 2 from nucleosome (PDB ID: 1AOI) ( b ).

Nucleosomal DNA was docked onto (MHF1-MHF2) 2 tetramer through alignment of MHF1-MHF2 dimer with H2A-H2B (PDB ID: 1AOI).

( a ) Comparisons of MHF with histones from nucleosome (PDB ID: 1AOI).

Publication Year: 2012


Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin.

(2013) Nat Commun 4

PubMed: 23715267 | PubMedCentral: PMC3674280 | DOI: 10.1038/ncomms2921

The nucleosome structure has been crystallized (PDB:1AOI) but without Doxo.

Publication Year: 2013


Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.

(2013) BMC Genomics 14

PubMed: 23805837 | PubMedCentral: PMC3700821 | DOI: 10.1186/1471-2164-14-428

( C ) Overlapping crystal structures for the nucleosome (PDB ID: 1AOI), GR (1R4O) and c-Jun|Fos (1FOS) showing GR can bind the nucleosome-occluded DNA while c-Jun|Fos has steric hindrances.

X-ray crystal structures of GR (PDB ID: 1R4O) and AP-1 (PDB ID: 1FOS) proteins bound to their canonical DNA motifs were overlaid with an X-ray structure of the histone octamer (PDB ID: 1AOI) bound to DNA (a nucleosome) using the program Chimera [ 31 ] to create a physical model of these proteins bound to the same DNA.

Publication Year: 2013


H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation.

(2013) PLoS Genet 9

PubMed: 23990805 | PubMedCentral: PMC3749939 | DOI: 10.1371/journal.pgen.1003725

The images were generated in Pymol using the following PDB files: 1AOI for canonical H2A-containing nucleosome structure and 1F66 for H2A.Z nucleosome structure.

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC3902957

A section of a structure of the nucleosome core particle of chromatin (to scale, with H3 in yellow) in complex with a 146 base pair DNA fragment is depicted on the left (PDB code 1AOI; Luger, K. et al... .

Publication Year: 2014


Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2.

(2014) Nucleic Acids Res 42

PubMed: 24259428 | PubMedCentral: PMC3936717 | DOI: 10.1093/nar/gkt1119

Intriguingly, the diameter and pitch of the formed P2 Cox spiral is virtually the same to how DNA wraps around nucleosome core particles, which also have a diameter and pitch of 65 ± 5 and 30 ... #x000b1; 5 Å, respectively, as measured on different nucleosomes (PDB codes 3AV1, 1AOI, 1EQZ, 1F66, 1M1A and 2CV5).

Publication Year: 2014


Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila.

(2014) Nucleic Acids Res 42

PubMed: 24598257 | PubMedCentral: PMC4027157 | DOI: 10.1093/nar/gku173

Modeling of JIL-1 The structure of JIL-1 was modeled with the I-TASSER protein prediction server ( 36 , 37 ) and compared to the crystal structure of a nucleosome (PDB ID: 1AOI).

Publication Year: 2014


Revealing transient structures of nucleosomes as DNA unwinds.

(2014) Nucleic Acids Res 42

PubMed: 24990379 | PubMedCentral: PMC4117781 | DOI: 10.1093/nar/gku562

The DNA component of the crystal structure for the nucleosome core particle (1AOI) was used to model the NCPs in the completely wrapped state.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4132697

Nucleosomes (blue and red) and RNA polymerase II (magenta) models were generated based on PDB accessions 1AOI and 1I6H, respectively.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4151707

Structure obtained from PDB 1AOI.

Publication Year: 2014


Synthetic epigenetics-towards intelligent control of epigenetic states and cell identity.

(2015) Clin Epigenetics 7

PubMed: 25741388 | PubMedCentral: PMC4347971 | DOI: 10.1186/s13148-015-0044-x

The structural models of the proteins were taken from PDB repository (zinc finger [PDB:1P47], TALE [PDB:2YPF], CRISPR/Cas9 [PDB:4OO8], M.HhaI [PDB:5MHT], Dnmt3a/3L [PDB:2QRV], TET2 [PDB:4NM6], nucleos... me [PDB:1AOI], a 21 amino acid linker was generated in PyMol, and 60 bp DNA sequence was generated with the make-na server ( http://structure.usc.edu/make-na/server.html )).

Publication Year: 2015


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4350607

394 Figure 17 Structural dissection of the X. laevis nucleosome core particle (PDB ID: 1AOI).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4513861

The structure is from 1AOI and accession number for the sequence is P02302.

Publication Year: 2015


The contribution of phosphate-phosphate repulsions to the free energy of DNA bending.

(2005) Nucleic Acids Res 33

PubMed: 15741179 | PubMedCentral: PMC552960 | DOI: 10.1093/nar/gki272

Toward this end, the first 71 bp (∼1 full turn of the superhelix) of the 146 bp histone-bound DNA strand from the crystal structure of a nucleosome core particle (PDB entry 1AOI ) ( 50 ) were ... xtracted and used as an initial structure for the bent DNA model.

2000 25 453 455 10973060 Figures and Tables Scheme 1 The 71 bp sequence used to model a full turn of DNA based on the crystallographic structure of a nucleosome core particle (PDB code 1AOI ) ( 50 ).

Publication Year: 2005