Primary Citation PubMed: 11092917
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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 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) ( ... 3 )] 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).
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.
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
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.
In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1.
(2005) BMC Bioinformatics 6 Suppl 4
PubMed: 16351741 | PubMedCentral: PMC1866393 | DOI: 10.1186/1471-2105-6-S4-S15
The H3-H4 histone dimer from Gallus gallus (PDB code: 1eqz) was chosen as a template.
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
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.
The configuration of nucleosome complexes of regular H2A histone and the variant H2A.Z histone are modeled using the crystal structures 1EQZ [ 78 ] and 1F66 [ 14 ] respectively.
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.
The nucleosome 1F66 corresponds to the recombinant mouse H2A.Z and recombinant Xenopus leavis H2B, H3 and H4, whereas 1EQZ refers to the chicken ( Gallus gallus ) histone octamer.
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.
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.
The color-coded ribbon diagram shows the dynamics of the dimers 1EQZ (I) and 1F66 (II) in the first (A) and second (B) global modes.
Superposition of the crystal structure with one conformation was generated by adding the fluctuation vector from the anisotropic fluctuation to the crystal coordinates for the dimers (I) 1EQZ and (II) 1F66 as shown in the front (A) and side views with respect to the dyad of the left nucleosome (B) and the right nucleosome (C) in the first slowest mode.
A complete nucleosome monomer with which the nucleosome complex was modeled was built using a nucleosome of the PDB database: 1F66 for variant nucleosome complex and 1EQZ for normal nucleosome complex.
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 ].
For the 1EQZ dimer, the cutoff distance is 35 Å for protein, 40 Å for DNA, and 45 for DNA-protein interaction.
Publication Year: 2007
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.
(2008) Nucleic Acids Res 36
PubMed: 18801847 | PubMedCentral: PMC2566867 | DOI: 10.1093/nar/gkn573
The largest of all histone clusters is composed of 113 residues (in the nucleosome core particle, PDB code: 1eqz, chain G; total protein chain length: 136), which is rather exceptional amongst the clu... ters being analyzed.
Publication Year: 2008
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 ).
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
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).
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
There are two structures of the nucleosome core particle (NCP) from Drosophila melanogaster (PDB id's 2NQB and 2PYO ), and one structure each of the NCP from chicken (PDB id 1EQZ ), mouse (PDB id 1U35... ) and human (PDB id 2NZD ).
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.
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.
Several structures have a kink at -1.5 or +1.5 ( 1EQZ ) as described earlier while some of them have kinks at -2 or +2.
The four steps are: an AT/AT step at SHL -1 in the structure 1EQZ (similar to the GG/CC kink into the minor groove, this is an unlikely conformation, since the AT/AT step favours nearly zero roll and slide in free B-DNA and other protein-bound DNA [ 25 ]), a GG/CC step at SHL -6 in the structure 1P3B , a CA/TG step at SHL -2 in the structure 2F8N and a CA/TG step at SHL -1 in the structure 2NZD .
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
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.
Monoubiquitinated histone H2A destabilizes photolesion-containing nucleosomes with concomitant release of UV-damaged DNA-binding protein E3 ligase.
(2012) J Biol Chem 287
PubMed: 22334663 | PubMedCentral: PMC3320950 | DOI: 10.1074/jbc.M111.307058
H2A is the only one of the four core histones with a significant C-terminal tail that is not a part of the histone-fold domain ( 70 ), and on the nucleosome core particle electron-density map (PDB cod... 1EQZ ) the tail is visible only to Leu-115, leaving the rest of the C-terminal residues disordered ( 71 ).
Publication Year: 2012
Inhibition of N-terminal lysines acetylation and transcription factor assembly by epirubicin induced deranged cell homeostasis.
(2012) PLoS One 7
PubMed: 23251640 | PubMedCentral: PMC3522591 | DOI: 10.1371/journal.pone.0051850
The crystal structures of the proteins were obtained from the Brookhaven protein data bank (PDB: 1EQZ, 453D).
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
PubMed ID is not available.
Published in 2015
( F ) VMD rendering (top) of TATTT residues 34–38 (yellow) and the complementary AAATA residues 672–753 (pink) from the 1EQZ pdb nucleosomal crystal structure, corresponding to peak ar... a from −40 to −36 in Figure 5E .
Publication Year: 2015
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