Primary Citation PubMed: 11101893
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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 ].
9 shows the superimposition of the ANM and crystal conformation of the 1F66 trimer.
The network for 1F66 tetramer was built using a cutoff distance of 40 Å for protein, 45 Å for DNA, and 50 Å to include the DNA-protein interaction.
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 superimposition of new ANM conformation and the crystal coordinates for the tetramer 1F66 is shown in 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.
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.
The color-coded diagram shows the dynamics of the 1F66 trimer in the first (A) and second (B) modes.
Superposition of crystal structure with one conformation was generated by adding the fluctuation vector from the anisotropic fluctuation to the crystal coordinates for the trimer 1F66 as shown in the front (A) and top (B) view in the first slowest mode.
1 shows the structure of variant nucleosome constructed using the PDB file 1F66 (Fig.
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.
7 depicts the color-coded diagram of the dynamics of 1F66 tetramer in the first and second slowest modes.
Superposition of crystal structure with one conformation was generated by adding the fluctuation vector from the anisotropic fluctuation to the crystal coordinates for the tetramer 1F66 as shown in the front (A) and right (B) side view in the first slowest mode.
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.
(A) The conformation of variant nucleosome constructed using the PDB file 1F66 deposited by Suto et al. .
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 color-coded ribbon diagram shows the dynamics of the 1F66 tetramer in the first (A) and second (B) global modes.
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.
For this analysis, the networks for 1F66 dimer and trimer were constructed using the cutoff distances 30 Å, 35 Å and 40 Å for the protein, DNA, and protein-DNA respectively.
For an easy understanding, the closest view of the color coded monomeric histone tetramer of the left side nucleosome in 1F66 dimer in the first global mode is shown (middle) in the subdiagram III and the secondary structures of the four histones (H3, H4, H2A.Z and H2B) are labeled individually.
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.
Publication Year: 2007
The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues.
(2009) BMC Evol Biol 9
PubMed: 19193230 | PubMedCentral: PMC2644675 | DOI: 10.1186/1471-2148-9-31
The 3D structures of H2A.Z-1 and H2A.Z-2 proteins from vertebrates as well as H2A.Z-e from early chordates were modeled using the coordinates determined for the crystal structure of a nucleosome parti... le containing the variant histone H2A.Z-1 from human (PDB accession code 1F66 ) as a reference [ 19 ].
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
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 ... F8N [ 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.
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.
Most of the fragments for all the structures in our dataset were observed to satisfy these criteria, with the minimum number of selected fragments being 99 out of 109 for the structure with PDB id 1F66 .
The remaining eighteen structures corresponding to sequence 5 display a variety of histone mutations and binding by different ligands: mutations in histones H3 and H4 (PDB id's 1P34 , 1P3A , 1P3B , 1P3F , 1P3G , 1P3I , 1P3K , 1P3L , 1P3M , 1P3O , 1P3P , 3C1B ), mutation in H2A to give H2A.Z (PDB id 1F66 ), presence of a linker joining the two DNA disks (PDB id 1S32 ), presence of groove binding ligands (PDB id's 1M18 , 1M19 , 1M1A ) and presence of an antigen bound to DNA (PDB id 1ZLA).
Thus at SHL -1.5 in the structure 1F66 , the roll value is -68.1° with corresponding tilt, twist, shift, slide and rise values of -4.3°, 43.0°, 0.3 Å, 1.2 Å and 4.7 Å respectively, while the GG/CC steps in 1KX4 at SHL ±1.5 provide examples of distortion without stretching, but with positive slide values.
Publication Year: 2011
Histone variant innovation in a rapidly evolving chordate lineage.
(2011) BMC Evol Biol 11
PubMed: 21756361 | PubMedCentral: PMC3156773 | DOI: 10.1186/1471-2148-11-208
PDB files of Oikopleura histone variants were viewed and aligned to PDB files of nucleosome crystal structures (PDB files 1kx5 and 1f66) in Pymol (Version 1.2r3pre, Schrödinger, LLC).
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.
H2A.Z.2.2 is an alternatively spliced histone H2A.Z variant that causes severe nucleosome destabilization.
(2012) Nucleic Acids Res 40
PubMed: 22467210 | PubMedCentral: PMC3401452 | DOI: 10.1093/nar/gks267
The starting point for molecular modeling was the crystal structure of a nucleosome core particle containing the histone variant H2A.Z (PDB 1F66) ( 50 ).
Publication Year: 2012
Database citation in full text biomedical articles.
(2013) PLoS One 8
PubMed: 23734176 | PubMedCentral: PMC3667078 | DOI: 10.1371/journal.pone.0063184
CT18, complete chromosome) PDB 39977 86000 0.46 1F66 (2.6 A Crystal structure of a nucleosome core particle containing the variant histone H2A.Z), 1LFD (Crystal structure of the active ras protein com... lexed with ras-interacting domain of ralgds) UniProt 9430 540000 ** 0.017 P02768 (Serum albumin), P04406 (Glyceraldehyde-3-phosphate dehydrogenase GAPDH) Total 209519 – – – * Total number of Annotations = Publisher-annotated + text-mined.
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.
Mutations in non-acid patch residues disrupt H2A.Z's association with chromatin through multiple mechanisms.
PubMed: 24098487 | PubMedCentral: PMC3788105 | DOI: 10.1371/journal.pone.0076394
Structural modelling In order to model the effect of mutations, the crystal structure of the mouse H2A.Z-containing nucleosome (PDB code 1F66) was used.
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
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