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Cryo-EM structure of the BRCA1-UBCH5C/BARD1 E3-E2 module bound to a nucleosome

Analyse Cryo-EM structure of the BRCA1-UBCH5C/BARD1 E3-E2 module bound to a nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JZV
Type: protein + DNA
Length: 1,371 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BRCA1,UBIQUITIN-conjugating enzyme E2 D3; BRCA1-associated ring domain protein 1; Histone…
EC: 2.3.2.23, 2.3.2.24, 2.3.2.27
UniProt: A0A386IN42, P61077, Q99728, Q6FI13, O60814, Q71DI3, P62805
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 56% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BRCA1,UBIQUITIN-conjugating enzyme E2 D3 (EC 2.3.2.23, 2.3.2.24, 2.3.2.27)	protein	253	36% helix, 14% strand	A0A386IN42, P61077
B	BRCA1-associated ring domain protein 1 (EC 2.3.2.27)	protein	97	52% helix, 10% strand	Q99728
N, n	Histone H2A type 2-a	protein	104	57% helix, 7% strand	Q6FI13
O	Histone H2B type 1-K	protein	94	70% helix, 4% strand	O60814
P	Histone H3.2	protein	90	68% helix, 4% strand	Q71DI3
Q	Histone H4	protein	87	57% helix, 8% strand	P62805
X	Widom 601 153-bp	dna	139	—	—
Y	Widom 601 153-bp	dna	139	—	—
o	Histone H2B type 1-K	protein	96	73% helix, 4% strand	O60814
p	Histone H3.2	protein	90	69% helix, 4% strand	Q71DI3
q	Histone H4	protein	78	62% helix, 9% strand	P62805

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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	921	0.84	0.86	106	empty
2	1169	0.82	0.84	116	empty
3	266	0.76	0.89	43	empty
4	298	0.69	0.84	30	empty
5	724	0.68	0.76	42	empty

Interfaces

43 interfaces between chains.

X–Y · 6235 Å² buried · 471 hydrogen bonds · nucleic-nucleic
P–Q · 2610 Å² buried · 25 hydrogen bonds · protein-protein
n–o · 2573 Å² buried · 22 hydrogen bonds · protein-protein
N–O · 2545 Å² buried · 17 hydrogen bonds · protein-protein
p–q · 2388 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7JZV · Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome · the same entry in another collection · chain q against q, 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 A0A386IN42
Every structure of UniProt P61077
Every structure of UniProt Q99728
Every structure of UniProt Q6FI13
Every structure of UniProt O60814
Every structure of UniProt Q71DI3
Every structure of UniProt P62805
Elsewhere: RCSB PDB 7JZV · PDBe 7JZV · UniProt A0A386IN42 · UniProt P61077 · UniProt Q99728 · UniProt Q6FI13 · UniProt O60814 · UniProt Q71DI3 · UniProt P62805

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