SMTL ID : 9e8l.1

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt4 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-mer

Ligands

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

ADP.1: 15 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, I.354, H.358, G.382, A.383, R.386 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.178, A:G.178, A:G.219, A:G.221, A:G.221, A:K.222, A:T.223, A:T.223, A:L.224 Salt bridges: A:K.222, A:K.222 ADP.2: 15 residues within 4Å: Chain B: 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 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.188, B:G.188, B:G.229, B:G.231, B:K.232, B:T.233, B:T.233, B:T.233, B:L.234, B:K.396 Salt bridges: B:K.232, B:K.232 ADP.3: 16 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, K.360 Ligands: MG.4 10 PLIP interactions: 10 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:L.198, C:N.296 Salt bridges: C:K.196 ADP.5: 13 residues within 4Å: Chain D: I.167, G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, G.372, A.373 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.168, D:G.168, D:P.208, D:P.208, D:C.210, D:G.211, D:K.212, D:T.213, D:T.213, D:M.214 Salt bridges: D:K.212

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain C: T.197, D.249 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.197 MG.7: 3 residues within 4Å: Chain E: T.181, D.233 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.181, E:D.233, E:D.233 MG.9: 5 residues within 4Å: Chain A: D.307, R.336 Chain F: T.234, D.286 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.234

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

ATP.6: 22 residues within 4Å: Chain E: E.134, I.135, G.136, L.138, P.175, 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 F: D.318, R.344, R.347 Ligands: MG.7 18 PLIP interactions: 4 interactions with chain F, 14 interactions with chain E Salt bridges: F:R.344, F:R.344, F:R.344, F:R.347, E:K.180, E:K.180 Hydrogen bonds: E:G.136, E:G.136, E:G.177, E:T.178, E:G.179, E:K.180, E:T.181, E:T.181, E:L.182, E:D.233, E:N.280, E:R.344 ATP.8: 21 residues within 4Å: Chain A: D.307, R.333, R.336 Chain F: D.187, I.188, G.189, 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.9 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.189, F:G.189, F:G.230, F:K.233, F:T.234, F:T.234, F:L.235, F:N.333 Salt bridges: F:K.233, F:K.233, A:R.333, A:R.333, A:R.333, A:R.336

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain 0: H.289 Chain V: H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain V Metal complexes: 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 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 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
substrate peptide: 1

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

1
v

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

substrate peptide

Related Entries With Identical Sequence