Research workbench

Cryo-EM structure of SET8-nucleosome complex

Analyse Cryo-EM structure of SET8-nucleosome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D1Z
Type: protein + DNA
Length: 1,219 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (145-mer)…
EC: 2.1.1.-, 2.1.1.361
UniProt: P68431, P62805, P04908, P06899, Q9NQR1
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 11 distinct chains · 56% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	97	68% helix, 4% strand	P68431
B	Histone H4	protein	81	63% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	107	57% helix, 6% strand	P04908
D	Histone H2B type 1-J	protein	93	75% helix, 4% strand	P06899
E	Histone H3.1	protein	97	65% helix, 4% strand	P68431
G	Histone H2A type 1-B/E	protein	109	53% helix, 6% strand	P04908
H	Histone H2B type 1-J	protein	92	76% helix, 4% strand	P06899
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—
K	Isoform 2 of N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.361)	protein	166	21% helix, 27% strand	Q9NQR1
F	Histone H4	protein	87	55% helix, 7% strand	P62805

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	901	0.81	0.83	78	empty
2	430	0.76	0.86	47	empty
3	1134	0.74	0.77	91	empty
4	326	0.72	0.85	36	empty
5	246	0.72	0.88	34	empty

Interfaces

42 interfaces between chains.

I–J · 6452 Å² buried · 490 hydrogen bonds · nucleic-nucleic
C–D · 2618 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2573 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 2562 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2504 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

7D1Z · Cryo-EM structure of SET8-nucleosome complex · the same entry in another collection · chain F against F, TM-score 1.00
P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain H against A, TM-score 0.99

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 P04908
Every structure of UniProt P06899
Every structure of UniProt Q9NQR1
Elsewhere: RCSB PDB 7D1Z · PDBe 7D1Z · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt Q9NQR1

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