SMTL ID : 9pdn.1

Nub1/Fat10-processing human 26S proteasome with Rpt1 at top of spiral staircase (AAA+ 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 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, D.249, E.250, I.328, H.332, G.356, A.357, K.360 Chain B: D.297, R.323, R.326 Ligands: MG.2 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.152, A:G.152, A:G.193, A:T.194, A:G.195, A:K.196, A:T.197, A:L.198, A:R.201, A:E.250, A:N.296, A:K.360 Salt bridges: A:K.196, A:K.196, B:R.323, B:R.323, B:R.323, B:R.326 ATP.6: 23 residues within 4Å: Chain K: D.176, V.177, G.178, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, R.227, N.322, I.354, H.358, G.382, A.383, R.386 Chain L: D.317, A.340, R.343, R.346 Ligands: MG.7 18 PLIP interactions: 14 interactions with chain K, 4 interactions with chain L Hydrogen bonds: K:G.178, K:G.219, K:T.220, K:T.220, K:T.220, K:G.221, K:K.222, K:T.223, K:L.224, K:R.227, K:N.322, K:R.386 Salt bridges: K:K.222, K:K.222, L:R.343, L:R.343, L:R.343, L:R.346 ATP.8: 22 residues within 4Å: Chain A: D.281, R.307, R.310 Chain L: 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.9 15 PLIP interactions: 11 interactions with chain L, 4 interactions with chain A Hydrogen bonds: L:G.188, L:G.188, L:G.229, L:T.230, L:G.231, L:K.232, L:T.233, L:L.234, L:N.332 Salt bridges: L:K.232, L:K.232, A:R.307, A:R.307, A:R.307, A:R.310 ATP.11: 21 residues within 4Å: Chain K: R.333, R.336 Chain N: D.187, I.188, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, D.286, N.333, I.365, H.369, G.393, A.394, K.397 Ligands: MG.12 15 PLIP interactions: 4 interactions with chain K, 11 interactions with chain N Salt bridges: K:R.333, K:R.333, K:R.333, K:R.336, N:K.233, N:K.233 Hydrogen bonds: N:G.189, N:G.189, N:G.230, N:G.232, N:K.233, N:T.234, N:T.234, N:L.235, N:E.287

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.197, D.249 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.197, A:D.249, A:D.249 MG.4: 4 residues within 4Å: Chain B: T.213, D.265, E.266 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.213, B:D.265 MG.7: 3 residues within 4Å: Chain K: T.223, D.275 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.223 MG.9: 3 residues within 4Å: Chain L: T.233, D.285 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.233 MG.12: 3 residues within 4Å: Chain N: T.234, D.286 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:T.234, N:D.286

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

ADP.3: 14 residues within 4Å: Chain B: G.168, M.170, G.209, C.210, G.211, K.212, T.213, M.214, I.344, I.348, G.372, A.373, N.376 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.168, B:G.168, B:G.209, B:C.210, B:G.211, B:K.212, B:T.213, B:M.214 Salt bridges: B:K.212 ADP.10: 15 residues within 4Å: Chain M: E.134, I.135, G.136, L.138, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316, G.340, A.341, R.344 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:G.136, M:G.136, M:G.177, M:T.178, M:G.179, M:K.180, M:T.181, M:T.181, M:T.181, M:L.182, M:R.344 Salt bridges: M:K.180

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain I: E.52, V.82, H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.113, I:H.115, I:D.126, I: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
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 7: K
26S proteasome regulatory subunit 4: 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
C

B
D

C
G

D
H

E
I

F
J

G
L

H
M

I
c

J
v

K
A

L
B

M
E

N
F

O
K

26S protease regulatory subunit 8

26S proteasome regulatory subunit 6B

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 7

26S proteasome regulatory subunit 4

26S protease regulatory subunit 10B

26S proteasome regulatory subunit 6A

Proteasome subunit alpha type-5

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