SMTL ID : 9e8i.1

Human proteasome in resting state conformation bound to TXNL1 in Forward conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: D.176, V.177, G.178, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, N.322, I.354, H.358, G.382, A.383 Chain B: D.317, R.343, R.346 Ligands: MG.2 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.178, A:G.178, A:G.219, A:T.220, A:G.221, A:K.222, A:T.223, A:L.224, A:N.322, B:D.317 Salt bridges: A:K.222, A:K.222, B:R.343, B:R.343, B:R.343, B:R.346 ATP.3: 21 residues within 4Å: Chain B: D.186, I.187, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, N.332, I.364, H.368, G.392, A.393, K.396 Chain C: D.281, R.307, R.310 Ligands: MG.4 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.188, B:G.188, B:G.229, B:T.230, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, B:N.332 Salt bridges: B:K.232, B:K.232, C:R.307, C:R.307, C:R.307, C:R.310 ATP.7: 20 residues within 4Å: Chain D: I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, E.266, N.312, I.344, I.348, G.372, A.373, N.376 Chain E: D.265, R.291, R.294 Ligands: MG.8 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:C.210, D:G.211, D:K.212, D:T.213, D:T.213, D:M.214, D:E.266, D:N.312 Salt bridges: D:K.212, D:K.212, E:R.291, E:R.291, E:R.291, E:R.294 ATP.9: 20 residues within 4Å: Chain E: E.134, I.135, G.136, 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 F: D.318, R.344, R.347 Ligands: MG.10 16 PLIP interactions: 12 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.136, E:G.136, E:G.177, E:T.178, E:T.178, E:G.179, E:K.180, E:T.181, E:L.182, E:N.280 Salt bridges: E:K.180, E:K.180, F:R.344, F:R.344, F:R.344, F:R.347 ATP.11: 23 residues within 4Å: Chain A: D.307, R.333, R.336 Chain F: D.187, I.188, G.189, L.191, P.229, 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.12 18 PLIP interactions: 14 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.189, F:G.189, F:G.230, F:T.231, F:T.231, F:G.232, F:K.233, F:T.234, F:L.235, F:R.238, F:N.333, F:N.333 Salt bridges: F:K.233, F:K.233, A:R.333, A:R.333, A:R.333, A:R.336

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.223, D.275 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.223 MG.4: 4 residues within 4Å: Chain B: T.233, D.285 Chain C: R.310 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.233 MG.6: 2 residues within 4Å: Chain C: D.249 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain D: T.213, D.265 Chain E: D.265, R.294 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.213 MG.10: 3 residues within 4Å: Chain E: T.181, D.233 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.181 MG.12: 5 residues within 4Å: Chain A: R.336 Chain F: T.234, D.286, E.287 Ligands: ATP.11 No protein-ligand interaction detected (PLIP)

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

ADP.5: 15 residues within 4Å: Chain C: M.150, I.151, G.152, P.192, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, G.356, A.357 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.152, C:G.152, C:G.193, C:T.194, C:G.195, C:K.196, C:T.197, C:T.197, C:T.197, C:L.198 Salt bridges: C:K.196

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 5 residues within 4Å: Chain V: E.52, H.113, H.115, S.123, D.126 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.52, V:H.113, V:H.115, V:D.126, V: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 proteasome regulatory subunit 4: B
26S protease regulatory subunit 8: C
26S proteasome regulatory subunit 6B: D
26S protease regulatory subunit 10B: E
26S proteasome regulatory subunit 6A: F
Proteasome subunit alpha type-6: G
Proteasome subunit alpha type-2: H
Proteasome subunit alpha type-4: I
Proteasome subunit alpha type-7: J
Proteasome subunit alpha type-5: K
Proteasome subunit alpha type-1: L
Proteasome subunit alpha type-3: M
26S proteasome non-ATPase regulatory subunit 1: N
26S proteasome non-ATPase regulatory subunit 3: O
26S proteasome non-ATPase regulatory subunit 12: P
26S proteasome non-ATPase regulatory subunit 11: Q
26S proteasome non-ATPase regulatory subunit 6: R
26S proteasome non-ATPase regulatory subunit 7: S
26S proteasome non-ATPase regulatory subunit 13: T
26S proteasome non-ATPase regulatory subunit 4: U
26S proteasome non-ATPase regulatory subunit 14: V
26S proteasome non-ATPase regulatory subunit 8: W
26S proteasome complex subunit SEM1: X
26S proteasome non-ATPase regulatory subunit 2: Y
Isoform 2 of NEDD8 ultimate buster 1: Z
Thioredoxin-like protein 1: 0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
U

O
V

P
W

Q
X

R
Y

S
Z

T
a

U
b

V
c

W
d

X
e

Y
f

Z
g

0
u

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S protease regulatory subunit 8

26S proteasome regulatory subunit 6B

26S protease regulatory subunit 10B

26S proteasome regulatory subunit 6A

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

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 3

26S proteasome non-ATPase regulatory subunit 12

26S proteasome non-ATPase regulatory subunit 11

26S proteasome non-ATPase regulatory subunit 6

26S proteasome non-ATPase regulatory subunit 7

26S proteasome non-ATPase regulatory subunit 13

26S proteasome non-ATPase regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 14

26S proteasome non-ATPase regulatory subunit 8

26S proteasome complex subunit SEM1

26S proteasome non-ATPase regulatory subunit 2

Isoform 2 of NEDD8 ultimate buster 1

Thioredoxin-like protein 1

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