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Cryo-EM structure of DOT1L and H2BK34UB-H3K79NLE nucleosome 2:1 complex

Analyse Cryo-EM structure of DOT1L and H2BK34UB-H3K79NLE nucleosome 2:1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7XCT
Type: protein + DNA
Length: 1,865 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; Histone H4; Histone H2A; Histone H2B type 1-K; Histone-lysine…
EC: 2.1.1.43
UniProt: P0CG47, A0A3P9NC92, Q08AJ9, O60814, Q8TEK3, S4RAZ3
Ligands: SAM
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 12 distinct chains · 44% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, N	Ubiquitin	protein	76	18% helix, 30% strand	P0CG47
F	Histone H4	protein	88	14% helix, 9% strand	A0A3P9NC92
G, C	Histone H2A	protein	108	54% helix, 6% strand	Q08AJ9
H	Histone H2B type 1-K	protein	92	75% helix, 4% strand	O60814
K	Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43)	protein	326	33% helix, 12% strand	Q8TEK3
E	Histone domain-containing protein	protein	98	64% helix, 2% strand	S4RAZ3
A	Histone domain-containing protein	protein	99	64% helix, 2% strand	S4RAZ3
D	Histone H2B type 1-K	protein	93	75% helix, 4% strand	O60814
B	Histone H4	protein	83	58% helix, 6% strand	A0A3P9NC92
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—
M	Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43)	protein	328	33% helix, 12% strand	Q8TEK3

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains K, E, M

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	930	0.83	0.84	79	empty
2	868	0.81	0.84	86	empty
3	915	0.78	0.81	85	empty
4	513	0.76	0.84	48	empty
5	525	0.74	0.83	55	empty

Interfaces

49 interfaces between chains.

I–J · 6720 Å² buried · 794 hydrogen bonds · nucleic-nucleic
F–E · 2672 Å² buried · 27 hydrogen bonds · protein-protein
D–C · 2590 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 2548 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 2537 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

7XCT · Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex · the same entry in another collection · chain N against N, 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 P0CG47
Every structure of UniProt A0A3P9NC92
Every structure of UniProt Q08AJ9
Every structure of UniProt O60814
Every structure of UniProt Q8TEK3
Every structure of UniProt S4RAZ3
Elsewhere: RCSB PDB 7XCT · PDBe 7XCT · UniProt P0CG47 · UniProt A0A3P9NC92 · UniProt Q08AJ9 · UniProt O60814 · UniProt Q8TEK3 · UniProt S4RAZ3

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