SMTL ID : 9e8n.1

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt3 at top of spiral staircase (locally refined on the AAA+ motor)

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: 18 residues within 4Å: Chain A: D.176, V.177, G.178, C.180, G.219, T.220, G.221, K.222, T.223, L.224, D.275, E.276, I.354, H.358, G.382, A.383, R.386 Chain L: R.346 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain L 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:E.276, A:R.386 Salt bridges: A:K.222, L:R.346 ADP.2: 15 residues within 4Å: Chain B: G.152, L.154, G.193, T.194, G.195, K.196, T.197, L.198, D.249, E.250, I.328, I.331, H.332, A.357, K.360 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.152, B:G.193, B:T.194, B:G.195, B:T.197, B:T.197, B:L.198, B:E.250 ADP.5: 19 residues within 4Å: Chain C: D.265, R.291, R.294 Chain K: G.168, M.170, G.206, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, I.348, G.372, A.373, N.376 17 PLIP interactions: 5 interactions with chain C, 12 interactions with chain K Hydrogen bonds: C:D.265, C:R.291, C:R.294, K:G.168, K:G.168, K:G.209, K:C.210, K:G.211, K:K.212, K:T.213, K:T.213, K:M.214, K:N.312, K:N.312, K:N.376 Salt bridges: C:R.291, C:R.294 ADP.6: 15 residues within 4Å: Chain L: 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 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:G.188, L:G.188, L:G.229, L:G.231, L:K.232, L:T.233, L:T.233, L:T.233, L:L.234, L:G.392 Salt bridges: L:K.232, L:K.232

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

ATP.3: 21 residues within 4Å: Chain C: E.134, I.135, G.136, L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, D.233, E.234, I.312, H.316, G.340, A.341 Chain M: D.318, R.344, R.347 Ligands: MG.4 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain M Hydrogen bonds: C:G.136, C:G.136, C:G.177, C:T.178, C:G.179, C:K.180, C:T.181, C:T.181, C:L.182, C:E.234 Salt bridges: C:K.180, C:K.180, M:R.344, M:R.344, M:R.344, M:R.347 ATP.7: 22 residues within 4Å: Chain A: D.307, R.333, R.336 Chain M: D.187, I.188, G.189, L.191, P.228, P.229, G.230, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, G.393, A.394, K.397 Ligands: MG.8 16 PLIP interactions: 12 interactions with chain M, 4 interactions with chain A Hydrogen bonds: M:G.189, M:G.230, M:T.231, M:T.231, M:G.232, M:K.233, M:T.234, M:T.234, M:L.235, M:N.333 Salt bridges: M:K.233, M:K.233, A:R.333, A:R.333, A:R.333, A:R.336

2 x MG: MAGNESIUM ION(Non-covalent)

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

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 3 residues within 4Å: Chain O: H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:H.113, 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

2024-12-04

Peptides

26S proteasome regulatory subunit 7: A
26S protease regulatory subunit 8: 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-1: H
Proteasome subunit alpha type-3: I
substrate: J
26S proteasome regulatory subunit 6B: K
26S proteasome regulatory subunit 4: L
26S proteasome regulatory subunit 6A: M
Proteasome subunit alpha type-5: N
26S proteasome non-ATPase regulatory subunit 14: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
H

E
J

F
K

G
L

H
M

I
N

J
v

K
D

L
B

M
F

N
P

O
c

26S proteasome regulatory subunit 7

26S protease regulatory subunit 8

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-1

Proteasome subunit alpha type-3

substrate

26S proteasome regulatory subunit 6B

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 6A

Proteasome subunit alpha type-5

26S proteasome non-ATPase regulatory subunit 14

Related Entries With Identical Sequence