SMTL ID : 9pf1.1

Nub1/Fat10-processing human 26S proteasome with Rpt4 at top of spiral staircase (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

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

ADP.1: 16 residues within 4Å: Chain A: D.176, V.177, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, I.354, H.358, G.382, A.383, R.386 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain K Hydrogen bonds: A:G.178, A:G.178, A:G.219, A:G.221, A:K.222, A:T.223, A:T.223, A:T.223, A:L.224, A:E.276, A:E.276, A:R.386 Salt bridges: A:K.222, A:K.222, K:R.343 ADP.2: 16 residues within 4Å: Chain B: M.150, G.152, P.191, P.192, G.193, T.194, G.195, K.196, T.197, L.198, D.249, N.296, I.328, H.332, A.357, K.360 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.152, B:G.152, B:G.193, B:T.194, B:G.195, B:K.196, B:T.197, B:N.296, B:N.296 Salt bridges: B:K.196 ADP.4: 16 residues within 4Å: Chain K: D.186, I.187, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:G.188, K:G.188, K:G.229, K:G.231, K:K.232, K:T.233, K:T.233, K:T.233, K:L.234, K:K.396 Salt bridges: K:K.232, K:K.232 ADP.5: 15 residues within 4Å: Chain L: G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, D.265, I.344, I.348, G.372, A.373, N.376 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.168, L:G.168, L:G.209, L:C.210, L:G.211, L:K.212, L:T.213, L:M.214, L:N.376 Salt bridges: L:K.212

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain I: H.113, H.115, W.121, S.123, D.126 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.113, I:H.115, I:D.126, I:D.126

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

ATP.6: 22 residues within 4Å: Chain M: E.134, I.135, G.136, L.138, P.175, P.176, G.177, T.178, G.179, K.180, T.181, L.182, E.234, N.280, I.312, H.316, G.340, A.341 Chain N: D.318, R.344, R.347 Ligands: MG.7 17 PLIP interactions: 12 interactions with chain M, 5 interactions with chain N Hydrogen bonds: M:G.136, M:G.136, M:G.177, M:T.178, M:G.179, M:T.181, M:T.181, M:L.182, M:N.280, M:R.344, N:D.318 Salt bridges: M:K.180, M:K.180, N:R.344, N:R.344, N:R.344, N:R.347 ATP.8: 21 residues within 4Å: Chain A: D.307, R.333, R.336 Chain N: D.187, I.188, G.189, G.230, T.231, G.232, K.233, T.234, L.235, R.238, E.287, N.333, I.365, H.369, G.393, A.394, K.397 Ligands: MG.9 18 PLIP interactions: 14 interactions with chain N, 4 interactions with chain A Hydrogen bonds: N:G.189, N:G.189, N:G.230, N:T.231, N:G.232, N:K.233, N:T.234, N:T.234, N:L.235, N:R.238, N:E.287, N:N.333 Salt bridges: N:K.233, N:K.233, A:R.333, A:R.333, A:R.333, A:R.336

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain M: T.181, D.233, E.234 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.181 MG.9: 3 residues within 4Å: Chain N: T.234, D.286 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:T.234, N:D.286

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
G

D
H

E
I

F
J

G
L

H
M

I
c

J
v

K
B

L
D

M
E

N
F

O
K

26S proteasome regulatory subunit 7

26S protease regulatory subunit 8

Proteasome subunit alpha type-6

Proteasome subunit alpha type-2

Proteasome subunit alpha type-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

26S proteasome non-ATPase regulatory subunit 14

Substrate polypeptide

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 6B

26S protease regulatory subunit 10B

26S proteasome regulatory subunit 6A

Proteasome subunit alpha type-5

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