SMTL ID : 9pdi.1

Nub1/Fat10-processing human 26S proteasome with Rpt2 at top of spiral staircase and partially unfolded Eos (AAA+ motor locally refined)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 23 residues within 4Å: Chain A: M.150, I.151, G.152, L.154, P.192, G.193, T.194, G.195, K.196, T.197, L.198, R.201, E.250, N.296, I.328, H.332, G.356, A.357, K.360 Chain B: D.297, R.323, R.326 Ligands: MG.2 20 PLIP interactions: 4 interactions with chain B, 16 interactions with chain A Salt bridges: B:R.323, B:R.323, B:R.323, B:R.326, A:K.196, A:K.196 Hydrogen bonds: A:G.152, A:G.152, A:G.193, A:T.194, A:G.195, A:K.196, A:T.197, A:T.197, A:L.198, A:R.201, A:E.250, A:N.296, A:N.296, A:K.360 ATP.7: 22 residues within 4Å: Chain A: D.281, R.307, R.310 Chain M: D.186, I.187, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, E.286, N.332, I.364, H.368, G.392, A.393, K.396 Ligands: MG.8 16 PLIP interactions: 12 interactions with chain M, 4 interactions with chain A Hydrogen bonds: M:G.188, M:G.188, M:G.229, M:T.230, M:G.231, M:K.232, M:T.233, M:L.234, M:N.332, M:N.332 Salt bridges: M:K.232, M:K.232, A:R.307, A:R.307, A:R.307, A:R.310

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.197, D.249, E.250 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.197 MG.4: 4 residues within 4Å: Chain B: T.213, D.265 Chain C: R.294 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.213 MG.8: 4 residues within 4Å: Chain M: T.233, D.285, E.286 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.233

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 20 residues within 4Å: Chain B: D.166, I.167, G.168, M.170, G.209, C.210, G.211, K.212, T.213, M.214, I.344, T.347, I.348, G.372, A.373, N.376 Chain C: D.265, R.291, R.294 Ligands: MG.4 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.168, B:G.168, B:G.209, B:C.210, B:G.211, B:K.212, B:T.213, B:T.213, B:M.214, C:D.265, C:R.294 Salt bridges: B:K.212, C:R.291, C:R.291 ADP.5: 16 residues within 4Å: Chain C: E.134, I.135, G.136, L.138, P.175, P.176, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316, G.340, R.344 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain N Hydrogen bonds: C:I.135, C:P.175, C:G.177, C:T.178, C:G.179, C:K.180, C:T.181, C:T.181, C:T.181, C:L.182, C:R.344, N:R.344 Salt bridges: C:K.180 ADP.6: 15 residues within 4Å: Chain L: D.176, V.177, G.178, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, I.354, H.358, G.382, R.386 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.178, L:G.178, L:G.219, L:G.221, L:K.222, L:T.223, L:T.223, L:L.224, L:R.386, L:R.386 Salt bridges: L:K.222 ADP.9: 16 residues within 4Å: Chain N: D.187, I.188, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, I.365, H.369, G.393, A.394, K.397 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:G.189, N:G.189, N:G.230, N:G.232, N:K.233, N:T.234, N:T.234, N:T.234, N:L.235, N:K.397 Salt bridges: N:K.233, N:K.233

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain O: E.52, H.113, H.115, S.123, D.126 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:H.113, O:H.115, O:H.115, O:D.126, O:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arkinson, C. et al., Structural landscape of the degrading 26S proteasome reveals conformation-specific binding of TXNL1. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-11-19

Peptides

26S protease regulatory subunit 8: A
26S proteasome regulatory subunit 6B: B
26S protease regulatory subunit 10B: C
Proteasome subunit alpha type-6: D
Proteasome subunit alpha type-2: E
Proteasome subunit alpha type-4: F
Proteasome subunit alpha type-7: G
Proteasome subunit alpha type-5: H
Proteasome subunit alpha type-1: I
Proteasome subunit alpha type-3: J
Substrate polypeptide: K
26S proteasome regulatory subunit 7: L
26S proteasome regulatory subunit 4: M
26S proteasome regulatory subunit 6A: N
26S proteasome non-ATPase regulatory subunit 14: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
G

E
H

F
I

G
J

H
K

I
L

J
M

K
v

L
A

M
B

N
F

O
c

26S protease regulatory subunit 8

26S proteasome regulatory subunit 6B

26S protease regulatory subunit 10B

Proteasome subunit alpha type-6

Proteasome subunit alpha type-2

Proteasome subunit alpha type-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-5

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Substrate polypeptide

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 6A

26S proteasome non-ATPase regulatory subunit 14

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