Research workbench

Cryo-EM structure of yeast cytoplasmic exosome

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

PDB: 5G06
Type: protein
Length: 3,420 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exosome complex component RRP45; Exosome complex component SKI6; Exosome complex…
EC: 3.1.13.1
UniProt: Q05636, P46948, P25359, P53256, Q12277, P48240, Q08285, P38792, P53859, Q08162, Q08491
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exosome complex component RRP45	protein	302	30% helix, 29% strand	Q05636
B	Exosome complex component SKI6	protein	240	29% helix, 30% strand	P46948
C	Exosome complex component RRP43	protein	335	26% helix, 30% strand	P25359
D	Exosome complex component RRP46	protein	223	34% helix, 37% strand	P53256
E	Exosome complex component RRP42	protein	265	24% helix, 33% strand	Q12277
F	Exosome complex component MTR3	protein	211	27% helix, 31% strand	P48240
G	Exosome complex component RRP40	protein	236	19% helix, 28% strand	Q08285
H	Exosome complex component RRP4	protein	293	23% helix, 25% strand	P38792
I	Exosome complex component CSL4	protein	227	4% helix, 47% strand	P53859
J	Exosome complex exonuclease DIS3 (EC 3.1.13.1)	protein	993	31% helix, 23% strand	Q08162
P	Superkiller protein 7	protein	95	60% helix, 0% strand	Q08491

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	1009	0.84	0.85	93	empty
2	1166	0.84	0.85	105	empty
3	199	0.82	0.95	37	empty
4	947	0.81	0.83	74	empty
5	662	0.79	0.84	56	empty

Interfaces

31 interfaces between chains.

C–F · 2097 Å² buried · 18 hydrogen bonds · protein-protein
B–J · 1947 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1917 Å² buried · 17 hydrogen bonds · protein-protein
E–H · 1904 Å² buried · 17 hydrogen bonds · protein-protein
F–I · 1557 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5G06 · Cryo-EM structure of yeast cytoplasmic exosome · the same entry in another collection · chain P against P, TM-score 1.00
P53256 · AlphaFold monomer V2.0 prediction for exosome complex component RRP46 (P53256) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 Q05636
Every structure of UniProt P46948
Every structure of UniProt P25359
Every structure of UniProt P53256
Every structure of UniProt Q12277
Every structure of UniProt P48240
Every structure of UniProt Q08285
Every structure of UniProt P38792
Every structure of UniProt P53859
Every structure of UniProt Q08162
Every structure of UniProt Q08491
Elsewhere: RCSB PDB 5G06 · PDBe 5G06 · UniProt Q05636 · UniProt P46948 · UniProt P25359 · UniProt P53256 · UniProt Q12277 · UniProt P48240 · UniProt Q08285 · UniProt P38792 · UniProt P53859 · UniProt Q08162 · UniProt Q08491

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