SMTL ID : 9e8g.1

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt5 at top of spiral staircase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: D.176, G.178, P.217, 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 B: D.317, R.343, R.346 Ligands: MG.2 16 PLIP interactions: 12 interactions with chain A, 4 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:R.227, A:R.386 Salt bridges: A:K.222, A:K.222, B:R.343, B:R.343, B:R.343, B:R.346 ATP.3: 22 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, E.286, N.332, I.364, H.368, G.392, A.393, K.396 Chain C: D.281, R.307, R.310 Ligands: MG.4 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain B Salt bridges: C:R.307, C:R.307, C:R.307, C:R.310, B:K.232, B:K.232 Hydrogen bonds: B:G.188, B:G.188, B:G.229, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, B:K.237, B:E.286, B:K.396 ATP.10: 22 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, E.287, N.333, I.365, H.369, G.393, A.394, K.397 Ligands: MG.11 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.189, F:G.189, F:G.230, F:G.232, F:K.233, F:T.234, F:T.234, F:L.235, F:N.333, F:K.397 Salt bridges: F:K.233, F:K.233, A:R.333, A:R.333, A:R.333, A:R.336

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.223 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.223 MG.4: 3 residues within 4Å: Chain B: T.233, D.285 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.233 MG.6: 3 residues within 4Å: Chain C: T.197, D.249 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.197 MG.8: 3 residues within 4Å: Chain D: T.213, D.265 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.213 MG.11: 3 residues within 4Å: Chain F: T.234, D.286 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.234, F:D.286

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

ADP.5: 19 residues within 4Å: Chain C: M.150, I.151, G.152, L.154, P.192, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, G.356, A.357, K.360 Chain D: D.297, R.323 Ligands: MG.6 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain C Salt bridges: D:R.323, D:R.323, C:K.196 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:L.198, C:K.360 ADP.7: 15 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, N.376 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.168, D:G.209, D:C.210, D:C.210, D:G.211, D:G.211, D:K.212, D:T.213, D:M.214, D:N.376 Salt bridges: D:K.212 ADP.9: 17 residues within 4Å: Chain E: E.134, I.135, G.136, L.138, G.177, T.178, G.179, K.180, T.181, L.182, D.233, E.234, I.312, H.316, G.340, A.341, R.344 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.136, E:G.136, E:G.177, E:G.179, E:K.180, E:T.181, E:T.181, E:T.181, E:E.234, E:E.234, E:R.344

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 5 residues within 4Å: Chain 1: V.82, H.113, H.115, D.126 Chain 7: H.289 5 PLIP interactions: 1 interactions with chain 7, 4 interactions with chain 1 Metal complexes: 7:H.289, 1:H.113, 1:H.115, 1:D.126, 1: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
Proteasome subunit beta type-6: N
Proteasome subunit beta type-7: O
Proteasome subunit beta type-3: P
Proteasome subunit beta type-2: Q
Proteasome subunit beta type-5: R
Proteasome subunit beta type-1: S
26S proteasome non-ATPase regulatory subunit 1: T
26S proteasome non-ATPase regulatory subunit 3: U
26S proteasome non-ATPase regulatory subunit 12: V
26S proteasome non-ATPase regulatory subunit 11: W
26S proteasome non-ATPase regulatory subunit 6: X
26S proteasome non-ATPase regulatory subunit 7: Y
26S proteasome non-ATPase regulatory subunit 13: Z
26S proteasome non-ATPase regulatory subunit 4: 0
26S proteasome non-ATPase regulatory subunit 14: 1
26S proteasome non-ATPase regulatory subunit 8: 2
26S proteasome complex subunit SEM1: 3
26S proteasome non-ATPase regulatory subunit 2: 4
Isoform 2 of NEDD8 ultimate buster 1: 5
Proteasome subunit beta type-4: 6
Thioredoxin-like protein 1: 7
substrate peptide: 8

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
N

O
P

P
Q

Q
R

R
S

S
T

T
U

U
V

V
W

W
X

X
Y

Y
Z

Z
a

0
b

1
c

2
d

3
e

4
f

5
g

6
h

7
u

8
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

Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-5

Proteasome subunit beta type-1

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

Proteasome subunit beta type-4

Thioredoxin-like protein 1

substrate peptide

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