Primary Citation PubMed: 20498094
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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
Contribution of histone N-terminal tails to the structure and stability of nucleosomes.
(2013) FEBS Open Bio 3
PubMed: 24251097 | PubMedCentral: PMC3821030 | DOI: 10.1016/j.fob.2013.08.007
of water molecules 0 0 0 0 RMSD from ideal Bond length (Å) 0.009 0.008 0.006 0.005 Bond angles (°) 1.31 1.27 1.15 1.06 Average B-factors (Å 2 ) Protein 86.5 90.6 99.9 89.5 DNA ... 49.7 154.7 162.9 152.3 Ion 111.8 76.3 80.1 75.1 PDB code 3W96 3W97 3W98 3W99 RMSD from wild type Cα (histones) (Å) 0.499 0.667 0.502 0.568 P (DNA) (Å) 0.703 0.897 0.627 0.749 a The crystal of the wild-type nucleosome (PDB 3AFA ) belongs to the space group P 2 1 2 1 2 1 , with unit cell dimensions a = 105.8, b = 109.5, c = 180.9 Å.
All structures were solved by the molecular replacement method with the program MOLREP [ 33 ], using the structure of the intact human nucleosome (Protein Data Bank code 3AFA ) as the search model.
All four tlH2A, tlH2B, tlH3, and tlH4 nucleosome crystals belonged to the space group P 2 1 2 1 2 1 , which is the same as the wt nucleosome crystal (PDB code 3AFA ), and the packing arrangements were almost identical among the four tailless nucleosomes.
Grey characters indicate residues that could not be modeled in the crystal structure of the wt nucleosome (PDB code 3AFA ) [ 28 , 30 ].
Publication Year: 2013
Scaffold functions of 14-3-3 adaptors in B cell immunoglobulin class switch DNA recombination.
(2013) PLoS One 8
PubMed: 24282540 | PubMedCentral: PMC3840166 | DOI: 10.1371/journal.pone.0080414
The CSR macromolecular complex localizes to chromatin S regions through 14-3-3 adaptors (green) binding to the modified histone tail H3K9acS10ph (PDB ID 2c1j) as well as to 5′-AGCT-3′ ... epeats (PDB ID 3afa), which specifically recur in S region DNA.
Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 24311584 | PubMedCentral: PMC3852653 | DOI: 10.1107/S090744491302252X
( a ) Superimposition of the H2A.Z.1 nucleosome on the canonical H2A nucleosome (PDB entry 3afa ; Tachiwana et al. , 2010 ▶ ).
The structures of the nucleosomes were determined by molecular replacement with Phaser (McCoy et al. , 2007 ▶ ) using the coordinates of the human nucleosome structure (PDB entry 3afa ; Tachiwana et al. , 2010 ▶ ) as the search model.
The atomic coordinates of the H2A nucleosome were obtained from the human H2A nucleosome structure (PDB entry 3afa ).
The B factors of the H2A nucleosome used for comparison were calculated from the canonical nucleosome structure (PDB entry 3afa ).
Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin.
(2013) Sci Rep 3
PubMed: 24336483 | PubMedCentral: PMC3863819 | DOI: 10.1038/srep03510
The crystal structure of the canonical nucleosome (PDB ID: 3AFA) is superimposed on the solution structures of the H2A and H2A.B octasomes.
Structure of human nucleosome containing the testis-specific histone variant TSH2B.
(2014) Acta Crystallogr F Struct Biol Commun 70
PubMed: 24699735 | PubMedCentral: PMC3976059 | DOI: 10.1107/S2053230X14004695
( a ) A close-up view around the canonical H2B Asn84 residue, which corresponds to the TSH2B Ser85 residue in the nucleosome (PDB entry 3afa ; Tachiwana et al. , 2010 ▶ ).
The structure of the TSH2B nucleosome was determined by molecular replacement with Phaser (McCoy et al. , 2007 ▶ ), using the coordinates of the human nucleosome structure (Tachiwana et al. , 2010 ▶ ; PDB entry 3afa ) as the search model.
Publication Year: 2014
A global assessment of cancer genomic alterations in epigenetic mechanisms.
(2014) Epigenetics Chromatin 7
PubMed: 25484917 | PubMedCentral: PMC4258301 | DOI: 10.1186/1756-8935-7-29
An aspartate was modeled at position 53 of H2B in the structure of the human nucleosome (PDB code 3AFA).
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