Primary Citation PubMed: 16001076
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Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone.
(2007) BMC Struct Biol 7
PubMed: 17996059 | PubMedCentral: PMC2216022 | DOI: 10.1186/1472-6807-7-76
Cross correlations between the motions of residues of dimers H3-H4 (A) and H2A-H2B (B) in the first nucleosomes in dimer 1EQZ (I), 1F66 (II) and 1ZBB (III) crystal structures.
The comparative analysis of cross-correlations shows that the constructed dimers 1F66 and 1EQZ have a similar correlation pattern as the nucleosome dimer 1ZBB [ 63 ].
3 describe the correlations between the motions of residues of dimers H3-H4 (A) and H2A-H2B (B) of 1EQZ (I), 1F66 (II) and 1ZBB (III) crystal structures in the first (Fig.
2 and 3 map the correlations between the residue motions of dimers H3-H4 and H2A (H2A.Z in 1F66 and H2A.1 in 1ZBB )-H2B (H2B.1 in 1ZBB ) for the three examined structures, labeled I-III.
Cross correlations between the motions of residues of dimers H3-H4 (A) and H2A-H2B (B) in the second nucleosomes in dimer 1EQZ (I), 1F66 (II) and 1ZBB (III) crystal structures; the amplitude of interactions follow the same color coding as Figure 2.
Because our main focus is on the analysis of the influence of H2A.Z over the dynamics, the interactions generated in H2A.1-H2B.1 motif of 1ZBB conformation have not been considered.
[ 63 ] reported the crystal structure of a tetranucleosome of Xenopus leavis origin at 9 Å resolution as solved by molecular replacement using the nucleosome core structure (PDB id: 1ZBB ).
In the case of H3-H4 dimers, the crystal structures 1EQZ , 1F66 and 1ZBB show a similar pattern of correlated and anti-correlated domain motions in both nucleosomes of the dimers.
The correlation map of dimers H3-H4 and H2A.1-H2B.1 would be different for the two nucleosomes present in 1ZBB if the second nucleosome had influence over the dynamics of the first nucleosome and vice versa.
Therefore, details regarding the influence of variant H2A.1 and H2B.1 (in 1ZBB ) over the global dynamics are beyond the scope of this article.
3 that the dynamics of the first and second nucleosomes possess similar domain interactions in 1ZBB .
Validation of the constructed model of 1EQZ , 1F66 dimers with 1ZBB dimers The comparison between the inter- and intra- domain motions of our model dimer and the dimer established by Schalch et al. (selected from the experimentally resolved tetromeric conformation) [ 63 ], confirms that the modeled nucleosome dimer of conventional and variant histones replicates the experimentally observed dimer conformation.
Publication Year: 2007
On the use of logarithmic scales for analysis of diffraction data.
(2009) Acta Crystallogr D Biol Crystallogr 65
PubMed: 19966414 | PubMedCentral: PMC2789003 | DOI: 10.1107/S0907444909039638
R (mvd, set 5) ( R PDB ) ( R ) ( R free ) ( R free R ) 0.67 2vb1 2vb1 0.0911 0.1090 0.1175 0.0089 0.670.76 1yk4 1r6j 2pve 0.1035 0.1199 0.1317 0.0121 0.760.87 2ol9 2h5c 2h5c 0.1158 0.1307 0.... 459 0.0153 0.871.00 1ob7 1rb9 1ixb 0.1281 0.1416 0.1601 0.0185 1.001.14 1iro 1iro 1z3n 0.1405 0.1525 0.1742 0.0217 1.141.31 2v9l 1n0q 2v9l 0.1528 0.1634 0.1884 0.0250 1.311.50 1hbz 2plz 1hbz 0.1651 0.1743 0.2026 0.0282 1.501.72 2ah2 6rxn 2pfg 0.1775 0.1851 0.2168 0.0314 1.721.97 1amk 2dya 2dya 0.1898 0.1960 0.2310 0.0346 1.972.25 2oh5 2oh5 2oh5 0.2021 0.2069 0.2452 0.0378 2.252.58 2oh7 1uvw 1uvw 0.2145 0.2178 0.2594 0.0410 2.582.95 5bna 1tre 1f4h 0.2268 0.2286 0.2736 0.0443 2.953.37 1bgj 1sv2 1ydz 0.2391 0.2395 0.2878 0.0475 3.373.86 2d3b 1gn3 2q3n 0.2515 0.2504 0.3020 0.0507 3.864.42 1aos 1veq 1veq 0.2638 0.2613 0.3162 0.0539 4.425.06 2rkj 1pgf 2rkj 0.2761 0.2721 0.3304 0.0571 5.065.80 3b5w 2b66 3b5x 0.2885 0.2830 0.3445 0.0603 5.806.63 2b9n 2b9n 3e3j 0.3008 0.2939 0.3587 0.0635 6.637.59 3c4y 3c4y 1yv0 0.3131 0.3048 0.3729 0.0668 7.598.69 2dh1 2dh1 2dh1 0.3255 0.3157 0.3871 0.0700 8.699.95 1vcr 1zbb 1vcr 0.3378 0.3265 0.4013 0.0732
Publication Year: 2009
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
To include the linker DNAs, 20 bp of DNA from the tetranucleosome structure ( 5 ) (PDB code 1zbb, 9 Å resolution), 10 bp at each entry/exit, were added to the reference... structure and the nucleosome structure obtained (which we will refer to as ‘nucleosome’) was used as an equilibrium conformation in the NMA.
To analyze the motions of the linker DNAs, the atoms from chains I (1–10) and J (347–338), corresponding to L-DNA1, and I (158–167) and J (181–190), corresponding to L-DNA2 (in the tetranucleosome structure 1zbb), were selected for comparison of the modes obtained for the nucleosome and the nucleosome+GH5 complex.
Publication Year: 2011
Nuclear hormone receptor co-repressors: structure and function.
(2012) Mol Cell Endocrinol 348
PubMed: 21925568 | PubMedCentral: PMC3315023 | DOI: 10.1016/j.mce.2011.08.033
A di-nucleosome (gray) is shown alongside the core complex highlighting the scale of the complex (PDB code 1ZBB ( Schalch et al., 2005 )).
Publication Year: 2012
Nucleosome spacing and chromatin higher-order folding.
PubMed: 22990522 | PubMedCentral: PMC3515531 | DOI: 10.4161/nucl.22168
For adding linker DNA, we used a DNA fragment from PDB 1ZBB.
Publication Year: null
The role of structural bioinformatics resources in the era of integrative structural biology.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 23633580 | PubMedCentral: PMC3640467 | DOI: 10.1107/S0907444913001157
of structures 86785 76355 † 9727 † 520 Highest resolution X-ray structure 0.48 ( 3nir ) Length of longest observed polymer chains Protein 3040 (... 3vkh ) 828 ( 2vda ) 1630 ( 3iyv and 1xi4 ) RNA 3206 ( 3o5h and 3o58 ) 111 ( 2lkr ) 3352 ( 3izf ) DNA 347 ( 1zbb ) 42 ( 2f1q ) 4896 ( 2ymf ) PDB entry with the highest number of Polymer residues 89160 (split over 4fy1 , 4fy2 , 4fy3 , 4fy4 , 4fy5 , 4fy6 , 4fy7 , 4fy8 , 4fy9 , 4fya ) Macromolecular atoms 717805 (split over 1voq , 1vor , 1vos , 1vou , 1vov , 1vow , 1vox , 1voy , 1voz , 1vp0 ) Macromolecular chains 480 (split over 4fy1 , 4fy2 , 4fy3 , 4fy4 , 4fy5 , 4fy6 , 4fy7 , 4fy8 , 4fy9 , 4fya ) No.
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.
New insights into the helical structure of 30-nm chromatin fibers.
(2014) Protein Cell 5
PubMed: 24969419 | PubMedCentral: PMC4085281 | DOI: 10.1007/s13238-014-0080-x
(A) The segmented cryo-EM density map (grey) for the tetra-nucleosomal unit in the 30-nm chromatin fibers reconstituted on 12 × 187 bp DNA, with a comparison to the X-r... y structure (PDB ID: 1ZBB, yellow) of the tetra-nucleosome (Schalch et al., 2005 ).
Publication Year: 2014
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