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Cryo-EM structure of unmodified nucleosome

Analyse Cryo-EM structure of unmodified nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7XD1
Type: protein + DNA
Length: 1,054 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3; Histone H4; Histone H2A type 1-B/E; DNA (147-mer); Histone H2B type 1-K
UniProt: A0A6I9KHI6, A0A0P9AXL3, P04908, O60814
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 8 distinct chains · 60% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	98	61% helix, 4% strand	A0A6I9KHI6
B	Histone H4	protein	80	61% helix, 9% strand	A0A0P9AXL3
C, G	Histone H2A type 1-B/E	protein	109	50% helix, 6% strand	P04908
E	Histone H3	protein	97	63% helix, 4% strand	A0A6I9KHI6
F	Histone H4	protein	79	59% helix, 9% strand	A0A0P9AXL3
I	DNA (147-mer)	dna	147	—	—
J	DNA (147-mer)	dna	147	—	—
D, H	Histone H2B type 1-K	protein	94	69% helix, 4% strand	O60814

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	1143	0.79	0.81	86	empty
2	395	0.74	0.85	49	empty
3	241	0.73	0.88	33	empty
4	234	0.72	0.88	33	empty
5	357	0.72	0.85	36	empty

Interfaces

33 interfaces between chains.

I–J · 6769 Å² buried · 733 hydrogen bonds · nucleic-nucleic
A–B · 2582 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 2568 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2566 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 2443 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

7XD1 · cryo-EM structure of unmodified nucleosome · the same entry in another collection · chain H against H, TM-score 1.00
P04908 · AlphaFold monomer V2.0 prediction for histone H2A type 1-B/E (P04908) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 A0A6I9KHI6
Every structure of UniProt A0A0P9AXL3
Every structure of UniProt P04908
Every structure of UniProt O60814
Elsewhere: RCSB PDB 7XD1 · PDBe 7XD1 · UniProt A0A6I9KHI6 · UniProt A0A0P9AXL3 · UniProt P04908 · UniProt O60814

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