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Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2AA and H2BA

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

PDB: 3X1T
Type: protein + DNA
Length: 1,053 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-a
UniProt: P68431, P62805, Q8CGP4, P70696
Ligands: MN, CL
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 62% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	DNA (146-mer)	dna	146	—	—
A, E	Histone H3.1	protein	98	65% helix, 4% strand	P68431
B	Histone H4	protein	81	60% helix, 9% strand	P62805
C	Histone H2A	protein	105	57% helix, 7% strand	Q8CGP4
D, H	Histone H2B type 1-a	protein	93	74% helix, 4% strand	P70696
F	Histone H4	protein	87	57% helix, 8% strand	P62805
G	Histone H2A	protein	106	57% helix, 7% strand	Q8CGP4

Ligands and binding sites

MN · Manganese (II) ion · metal · 22 copies · chains I, J, A, C, D, G, H
CL · Chloride ion · ion · 8 copies · chains J, I, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	791	0.79	0.83	79	empty
2	432	0.77	0.86	58	empty
3	503	0.77	0.85	61	CL
4	595	0.70	0.79	66	empty
5	339	0.66	0.81	36	empty

Interfaces

37 interfaces between chains.

I–J · 6428 Å² buried · 555 hydrogen bonds · nucleic-nucleic
E–F · 2686 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2640 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 2621 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2565 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3X1T · Crystal structure of nucleosome core particle consisting of mouse testis specific histone… · the same entry in another collection · chain H against H, TM-score 1.00
P70696 · AlphaFold monomer V2.0 prediction for histone H2B type 1-a (P70696) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P70696
Elsewhere: RCSB PDB 3X1T · PDBe 3X1T · UniProt P68431 · UniProt P62805 · UniProt Q8CGP4 · UniProt P70696

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