Research workbench

Human nuclear exosome targeting (next) complex homodimer bound to RNA (substrate 1)

Analyse Human nuclear exosome targeting (next) complex homodimer bound to RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7S7B
Type: protein + RNA
Length: 2,731 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exosome RNA helicase MTR4; Zinc finger cchc domain-containing protein 8,ZINC finger cchc…
EC: 3.6.4.13
UniProt: P42285, Q6NZY4, Q9Y580
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 5 distinct chains · 40% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Exosome RNA helicase MTR4 (EC 3.6.4.13)	protein	924	47% helix, 15% strand	P42285
B	Zinc finger cchc domain-containing protein 8,ZINC finger cchc domain-containing protein 8	protein	351	33% helix, 9% strand	Q6NZY4
C, G	RNA-binding protein 7	protein	79	24% helix, 25% strand	Q9Y580
D, H	RNA (46-mer)	rna	11	—	—
F	Zinc finger cchc domain-containing protein 8,ZINC finger cchc domain-containing protein 8	protein	352	32% helix, 9% strand	Q6NZY4

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, F

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	748	0.81	0.85	73	empty
2	307	0.80	0.91	48	empty
3	339	0.79	0.89	52	empty
4	728	0.75	0.80	67	empty
5	1132	0.75	0.77	102	empty

Interfaces

13 interfaces between chains.

A–B · 5557 Å² buried · 45 hydrogen bonds · protein-protein
E–F · 5497 Å² buried · 45 hydrogen bonds · protein-protein
B–F · 4595 Å² buried · 40 hydrogen bonds · protein-protein
E–H · 1332 Å² buried · 32 hydrogen bonds · protein-nucleic
B–C · 1304 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

7S7B · Human Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1) · the same entry in another collection · chain H against H, TM-score 1.00
Q9Y580 · AlphaFold monomer V2.0 prediction for RNA-binding protein 7 (Q9Y580) · a predicted model of the same protein · chain C against A, TM-score 0.95
P42285 · AlphaFold monomer V2.0 prediction for exosome RNA helicase MTR4 (P42285) · a predicted model of the same protein · chain A against A, TM-score 0.84
Q6NZY4 · AlphaFold monomer V2.0 prediction for zinc finger cchc domain- containing protein 8… · a predicted model of the same protein · chain B against A, TM-score 0.31

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 P42285
Every structure of UniProt Q6NZY4
Every structure of UniProt Q9Y580
Elsewhere: RCSB PDB 7S7B · PDBe 7S7B · UniProt P42285 · UniProt Q6NZY4 · UniProt Q9Y580

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