Research workbench

Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid

Analyse Formation of an intricate helical bundle dictates the assembly of the 26S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J47
Type: protein
Length: 308 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 7.4
Source: Saccharomyces cerevisiae
Molecule: 26S proteasome regulatory subunit RPN11; 26S proteasome regulatory subunit RPN8; 26S…
UniProt: P43588, Q08723, Q04062, Q12250, Q12377, Q06103, P40016, P32496
Pockets: 4 · best druggability 0.82

Structure

electron microscopy · resolution 7.4 · 8 distinct chains · 93% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V	26S proteasome regulatory subunit RPN11	protein	63	94% helix, 0% strand	P43588
U	26S proteasome regulatory subunit RPN8	protein	91	93% helix, 0% strand	Q08723
O	26S proteasome regulatory subunit RPN9	protein	28	93% helix, 0% strand	Q04062
P	26S proteasome regulatory subunit RPN5	protein	34	94% helix, 0% strand	Q12250
Q	26S proteasome regulatory subunit RPN6	protein	25	92% helix, 0% strand	Q12377
R	26S proteasome regulatory subunit RPN7	protein	26	92% helix, 0% strand	Q06103
S	26S proteasome regulatory subunit RPN3	protein	24	92% helix, 0% strand	P40016
T	26S proteasome regulatory subunit RPN12	protein	17	88% helix, 0% strand	P32496

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1087	0.82	0.83	81	empty
2	139	0.59	0.83	21	empty
3	115	0.41	0.75	23	empty
4	60	0.28	0.74	18	empty

Interfaces

18 interfaces between chains.

V–U · 1251 Å² buried · 34 hydrogen bonds · protein-protein
U–P · 1004 Å² buried · 13 hydrogen bonds · protein-protein
U–O · 832 Å² buried · 3 hydrogen bonds · protein-protein
U–S · 777 Å² buried · 12 hydrogen bonds · protein-protein
Q–R · 596 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 isopeptide (isopeptide).

Compared structures

3J47 · Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid · the same entry in another collection · chain V against V, TM-score 1.00
P32496 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN12 (P32496) · a predicted model of the same protein · chain T against A, TM-score 0.89
Q12377 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN6 (Q12377) · a predicted model of the same protein · chain Q against A, TM-score 0.87
Q08723 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN8 (Q08723) · a predicted model of the same protein · chain U against A, TM-score 0.87
Q12250 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN5 (Q12250) · a predicted model of the same protein · chain P against A, TM-score 0.85

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 P43588
Every structure of UniProt Q08723
Every structure of UniProt Q04062
Every structure of UniProt Q12250
Every structure of UniProt Q12377
Every structure of UniProt Q06103
Every structure of UniProt P40016
Every structure of UniProt P32496
Elsewhere: RCSB PDB 3J47 · PDBe 3J47 · UniProt P43588 · UniProt Q08723 · UniProt Q04062 · UniProt Q12250 · UniProt Q12377 · UniProt Q06103 · UniProt P40016 · UniProt P32496

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