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Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming

Analyse Crystal structure of nucleosome core particle in the presence of histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3X1U
Type: protein + DNA
Length: 1,061 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (146-mer); Histone H3.1; Histone H4; Histone H2A; Histone H2B type 1-B
UniProt: P68431, P62805, Q8CGP4, P33778
Ligands: MN, CL
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 8 distinct chains · 60% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	DNA (146-mer)	dna	146	—	—
A	Histone H3.1	protein	98	61% helix, 4% strand	P68431
B	Histone H4	protein	83	59% helix, 8% strand	P62805
C	Histone H2A	protein	105	54% helix, 7% strand	Q8CGP4
D, H	Histone H2B type 1-B	protein	94	71% helix, 4% strand	P33778
E	Histone H3.1	protein	99	65% helix, 4% strand	P68431
F	Histone H4	protein	87	57% helix, 8% strand	P62805
G	Histone H2A	protein	109	53% helix, 5% strand	Q8CGP4

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains I, E, F, G, H
CL · Chloride ion · ion · 6 copies · chains I, J, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	862	0.84	0.86	91	empty
2	683	0.78	0.83	62	empty
3	1011	0.73	0.77	65	empty
4	673	0.71	0.79	53	empty
5	1147	0.71	0.75	99	empty

Interfaces

36 interfaces between chains.

I–J · 6316 Å² buried · 525 hydrogen bonds · nucleic-nucleic
E–F · 2634 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2610 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 2576 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2557 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3X1U · Crystal structure of nucleosome core particle in the presence of histone variants… · the same entry in another collection · chain H against H, TM-score 1.00
P33778 · AlphaFold monomer V2.0 prediction for histone H2B type 1-B (P33778) · a predicted model of the same protein · chain D against A, TM-score 0.89

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P68431
Every structure of UniProt P62805
Every structure of UniProt Q8CGP4
Every structure of UniProt P33778
Elsewhere: RCSB PDB 3X1U · PDBe 3X1U · UniProt P68431 · UniProt P62805 · UniProt Q8CGP4 · UniProt P33778

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