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Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the compact active state

Analyse Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the compact… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C23
Type: protein
Length: 1,823 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polycomb protein SUZ12; Protein jumonji; Histone-lysine N-methyltransferase EZH2…
EC: 2.1.1.43
UniProt: Q15022, Q92833, Q15910, O75530, Q09028, Q6ZN18
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 12 distinct chains · 19% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polycomb protein SUZ12	protein	123	11% helix, 15% strand	Q15022
E	Protein jumonji	protein	27	22% helix, 4% strand	Q92833
K	Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43)	protein	325	22% helix, 14% strand	Q15910
L	Polycomb protein eed	protein	362	5% helix, 37% strand	O75530
M	Polycomb protein SUZ12	protein	122	61% helix, 3% strand	Q15022
N	Histone-binding protein RBBP4	protein	386	9% helix, 31% strand	Q09028
O	JARID2-substrate	protein	7	0% helix, 14% strand	—
P	Zinc finger protein AEBP2	protein	64	23% helix, 0% strand	Q6ZN18
Q	Polycomb protein SUZ12	protein	66	33% helix, 0% strand	Q15022
Z	SUZ12	protein	135	0% helix, 18% strand	—
C	Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43)	protein	193	42% helix, 6% strand	Q15910
B	Protein jumonji	protein	13	31% helix, 0% strand	Q92833

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1173	0.85	0.86	141	empty
2	387	0.85	0.94	50	empty
3	847	0.81	0.83	92	empty
4	732	0.81	0.84	83	empty
5	473	0.76	0.84	37	empty

Interfaces

30 interfaces between chains.

L–C · 3525 Å² buried · 37 hydrogen bonds · protein-protein
K–M · 2651 Å² buried · 31 hydrogen bonds · protein-protein
N–Q · 1596 Å² buried · 25 hydrogen bonds · protein-protein
A–N · 1516 Å² buried · 21 hydrogen bonds · protein-protein
K–C · 1270 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 modified (disulfide, methylation).

Compared structures

6C23 · Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State · the same entry in another collection · chain B against B, 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 Q15022
Every structure of UniProt Q92833
Every structure of UniProt Q15910
Every structure of UniProt O75530
Every structure of UniProt Q09028
Every structure of UniProt Q6ZN18
Elsewhere: RCSB PDB 6C23 · PDBe 6C23 · UniProt Q15022 · UniProt Q92833 · UniProt Q15910 · UniProt O75530 · UniProt Q09028 · UniProt Q6ZN18

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