SMTL ID : 9pdl.1

Nub1/Fat10-processing human 26S proteasome with Rpt5 at top of spiral staircase (AAA+ locally refined)

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

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

ADP.1: 19 residues within 4Å: Chain A: M.150, I.151, G.152, L.154, P.192, G.193, T.194, G.195, K.196, T.197, L.198, R.201, I.328, H.332, G.356, A.357 Chain L: D.297, R.323 Ligands: MG.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain L Hydrogen bonds: A:G.152, A:G.193, A:T.194, A:T.194, A:G.195, A:K.196, A:T.197, A:T.197, A:L.198, A:R.201 Salt bridges: A:K.196, L:R.323, L:R.323 ADP.8: 16 residues within 4Å: Chain L: D.166, 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.9 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.168, L:G.168, L:G.209, L:C.210, L:G.211, L:K.212, L:T.213, L:T.213, L:M.214, L:N.376 Salt bridges: L:K.212 ADP.10: 17 residues within 4Å: Chain M: E.134, I.135, G.136, L.138, G.177, T.178, G.179, K.180, T.181, L.182, E.234, I.312, I.315, H.316, G.340, A.341, R.344 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:G.136, M:G.136, M:G.177, M:G.179, M:K.180, M:T.181, M:T.181, M:T.181, M:E.234, M:R.344

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.197, D.249 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.197 MG.5: 3 residues within 4Å: Chain J: T.223, D.275 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.223 MG.7: 4 residues within 4Å: Chain K: T.233, D.285, E.286 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.233 MG.9: 3 residues within 4Å: Chain L: T.213, D.265 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.213 MG.12: 4 residues within 4Å: Chain J: R.336 Chain N: T.234, D.286 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.234

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain H: E.52, V.82, H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.113, H:H.115, H:D.126, H:D.126

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

ATP.4: 22 residues within 4Å: Chain J: D.176, V.177, G.178, C.180, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, N.322, I.354, H.358, G.382, A.383, R.386 Chain K: D.317, R.343, R.346 Ligands: MG.5 16 PLIP interactions: 12 interactions with chain J, 4 interactions with chain K Hydrogen bonds: J:G.178, J:G.219, J:T.220, J:T.220, J:T.220, J:G.221, J:K.222, J:T.223, J:L.224, J:N.322 Salt bridges: J:K.222, J:K.222, K:R.343, K:R.343, K:R.343, K:R.346 ATP.6: 22 residues within 4Å: Chain A: D.281, R.307, R.310 Chain K: 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 Ligands: MG.7 16 PLIP interactions: 12 interactions with chain K, 4 interactions with chain A Hydrogen bonds: K:G.188, K:G.188, K:G.229, K:T.230, K:G.231, K:K.232, K:T.233, K:L.234, K:E.286, K:K.396 Salt bridges: K:K.232, K:K.232, A:R.307, A:R.307, A:R.307, A:R.310 ATP.11: 22 residues within 4Å: Chain J: D.307, R.333, R.336 Chain N: 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.12 16 PLIP interactions: 12 interactions with chain N, 4 interactions with chain J Hydrogen bonds: N:G.189, N:G.189, N:G.230, N:T.231, N:T.231, N:G.232, N:K.233, N:T.234, N:T.234, N:L.235 Salt bridges: N:K.233, N:K.233, J:R.333, J:R.333, J:R.333, J:R.336

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

2025-11-19

Peptides

26S protease regulatory subunit 8: A
Proteasome subunit alpha type-6: B
Proteasome subunit alpha type-2: C
Proteasome subunit alpha type-4: D
Proteasome subunit alpha type-7: E
Proteasome subunit alpha type-1: F
Proteasome subunit alpha type-3: G
26S proteasome non-ATPase regulatory subunit 14: H
Substrate polypeptide: I
26S proteasome regulatory subunit 7: J
26S proteasome regulatory subunit 4: K
26S proteasome regulatory subunit 6B: L
26S protease regulatory subunit 10B: M
26S proteasome regulatory subunit 6A: N
Proteasome subunit alpha type-5: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
G

C
H

D
I

E
J

F
L

G
M

H
c

I
v

J
A

K
B

L
D

M
E

N
F

O
K

26S protease regulatory subunit 8

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

26S proteasome non-ATPase regulatory subunit 14

Substrate polypeptide

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 6B

26S protease regulatory subunit 10B

26S proteasome regulatory subunit 6A

Proteasome subunit alpha type-5

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