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Cryo-EM structure of the human INO80 complex bound to nucleosome

Analyse Cryo-EM structure of the human INO80 complex bound to nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HTS
Type: protein + DNA
Length: 4,753 residues
Chains: 19
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.8
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: RuvB-like 1; RuvB-like 2; Chromatin-remodeling ATPase INO80; Actin-related protein 5…
EC: 3.6.4.12, 3.6.4.-
UniProt: Q9Y265, Q9Y230, Q9ULG1, Q9H9F9, P68431, P62805, P04908, P06899, Q9C086
Ligands: ADP, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 4.8 · 18 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RuvB-like 1 (EC 3.6.4.12)	protein	434	40% helix, 24% strand	Q9Y265
B	RuvB-like 2 (EC 3.6.4.12)	protein	429	39% helix, 24% strand	Q9Y230
C	RuvB-like 1 (EC 3.6.4.12)	protein	437	40% helix, 24% strand	Q9Y265
D, F	RuvB-like 2 (EC 3.6.4.12)	protein	434	38% helix, 24% strand	Q9Y230
E	RuvB-like 1 (EC 3.6.4.12)	protein	443	40% helix, 23% strand	Q9Y265
G	Chromatin-remodeling ATPase INO80 (EC 3.6.4.-)	protein	680	41% helix, 10% strand	Q9ULG1
H	Actin-related protein 5	protein	326	47% helix, 16% strand	Q9H9F9
I	Histone H3.1	protein	96	69% helix, 4% strand	P68431
J	Histone H4	protein	82	56% helix, 6% strand	P62805
K	Histone H2A type 1-B/E	protein	106	56% helix, 2% strand	P04908
L	Histone H2B type 1-J	protein	96	75% helix, 1% strand	P06899
M	Histone H3.1	protein	99	67% helix, 4% strand	P68431
N	Histone H4	protein	86	57% helix, 6% strand	P62805
O	Histone H2A type 1-B/E	protein	105	56% helix, 1% strand	P04908
P	Histone H2B type 1-J	protein	94	77% helix, 0% strand	P06899
R	INO80 complex subunit B	protein	72	14% helix, 25% strand	Q9C086
X	DNA (150-mer)	dna	150	—	—
Y	DNA (150-mer)	dna	150	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · chains R

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	1082	0.90	0.91	143	empty
2	602	0.86	0.91	60	empty
3	294	0.83	0.94	45	ADP
4	939	0.82	0.84	99	empty
5	489	0.82	0.89	63	ADP

Interfaces

62 interfaces between chains.

X–Y · 6762 Å² buried · 588 hydrogen bonds · nucleic-nucleic
A–F · 3990 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 3584 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 3544 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 3538 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

6HTS · Cryo-EM structure of the human INO80 complex bound to nucleosome · the same entry in another collection · chain J against J, TM-score 1.00

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 Q9Y265
Every structure of UniProt Q9Y230
Every structure of UniProt Q9ULG1
Every structure of UniProt Q9H9F9
Every structure of UniProt P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt P06899
Every structure of UniProt Q9C086
Elsewhere: RCSB PDB 6HTS · PDBe 6HTS · UniProt Q9Y265 · UniProt Q9Y230 · UniProt Q9ULG1 · UniProt Q9H9F9 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt Q9C086

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