SMTL ID : 9e8n.1

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt3 at top of spiral staircase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: D.176, V.177, G.178, C.180, G.219, T.220, G.221, K.222, T.223, L.224, D.275, I.354, H.358, G.382, A.383, R.386 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.178, A:G.219, A:T.220, A:G.221, A:K.222, A:T.223, A:T.223, A:L.224, A:D.275, A:R.386 Salt bridges: A:K.222, A:K.222 ADP.2: 12 residues within 4Å: Chain B: G.193, T.194, G.195, K.196, T.197, L.198, R.213, D.249, I.328, H.332, A.357, K.360 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.193, B:G.195, B:T.197, B:T.197, B:L.198, B:R.213, B:D.249 ADP.3: 19 residues within 4Å: Chain C: D.166, I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, D.265, N.312, I.344, I.348, G.372, A.373, N.376 Chain V: R.291, R.294 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain V Hydrogen bonds: C:I.167, C:G.209, C:T.213, C:M.214, C:D.265, C:N.312, V:D.265, V:R.291, V:R.294 Salt bridges: C:K.212, V:R.291, V:R.291, V:R.294 ADP.4: 15 residues within 4Å: Chain T: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 11 PLIP interactions: 11 interactions with chain T Hydrogen bonds: T:G.188, T:G.188, T:G.229, T:G.231, T:K.232, T:T.233, T:T.233, T:T.233, T:L.234 Salt bridges: T:K.232, T:K.232

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

ATP.5: 23 residues within 4Å: Chain V: E.134, I.135, G.136, L.138, P.175, P.176, G.177, T.178, G.179, K.180, T.181, L.182, D.233, N.280, I.312, H.316, G.340, A.341, R.344 Chain W: D.318, R.344, R.347 Ligands: MG.6 18 PLIP interactions: 14 interactions with chain V, 4 interactions with chain W Hydrogen bonds: V:G.136, V:G.136, V:G.177, V:T.178, V:G.179, V:K.180, V:T.181, V:T.181, V:T.181, V:L.182, V:N.280, V:R.344 Salt bridges: V:K.180, V:K.180, W:R.344, W:R.344, W:R.344, W:R.347 ATP.7: 20 residues within 4Å: Chain A: D.307, R.333, R.336 Chain W: D.187, I.188, G.189, 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 W, 4 interactions with chain A Hydrogen bonds: W:G.189, W:G.189, W:G.230, W:T.231, W:G.232, W:K.233, W:T.234, W:T.234, W:L.235, W:N.333 Salt bridges: W:K.233, W:K.233, A:R.333, A:R.333, A:R.333, A:R.336

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain V: T.181, D.233 Ligands: ATP.5 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:T.181, V:D.233, V:D.233 MG.8: 4 residues within 4Å: Chain A: R.336 Chain W: T.234, D.286 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:T.234, W:D.286

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain R: H.289 Chain X: H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:H.113, X:H.115, X:D.126, X:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arkinson, C. et al., Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1. Biorxiv (2024)

Release Date

2024-12-04

Peptides

26S proteasome regulatory subunit 7: A
26S protease regulatory subunit 8: B
26S proteasome regulatory subunit 6B: 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
Proteasome subunit beta type-7: J
26S proteasome non-ATPase regulatory subunit 12: K
26S proteasome non-ATPase regulatory subunit 11: L
26S proteasome non-ATPase regulatory subunit 6: M
26S proteasome non-ATPase regulatory subunit 13: N
26S proteasome non-ATPase regulatory subunit 4: O
26S proteasome non-ATPase regulatory subunit 8: P
Isoform 2 of NEDD8 ultimate buster 1: Q
Thioredoxin-like protein 1: R
substrate: S
26S proteasome regulatory subunit 4: T
26S proteasome non-ATPase regulatory subunit 7: U
26S protease regulatory subunit 10B: V
26S proteasome regulatory subunit 6A: W
26S proteasome non-ATPase regulatory subunit 14: X
Proteasome subunit alpha type-5: Y
26S proteasome complex subunit SEM1: Z
26S proteasome non-ATPase regulatory subunit 1: 0
26S proteasome non-ATPase regulatory subunit 2: 1
26S proteasome non-ATPase regulatory subunit 3: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
G

E
H

F
I

G
J

H
L

I
M

J
O

K
W

L
X

M
Y

N
a

O
b

P
d

Q
g

R
u

S
v

T
B

U
Z

V
E

W
F

X
c

Y
K

Z
e

0
U

1
f

2
V

26S proteasome regulatory subunit 7

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

Proteasome subunit beta type-7

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 13

26S proteasome non-ATPase regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 8

Isoform 2 of NEDD8 ultimate buster 1

Thioredoxin-like protein 1

substrate

26S proteasome regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 7

26S protease regulatory subunit 10B

26S proteasome regulatory subunit 6A

26S proteasome non-ATPase regulatory subunit 14

Proteasome subunit alpha type-5

26S proteasome complex subunit SEM1

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 2

26S proteasome non-ATPase regulatory subunit 3

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