SMTL ID : 8jri.1

Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) without any bound substrate.

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-mer

Ligands

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

ATP.1: 20 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, I.357, H.358, G.382, A.383, R.386 Chain B: D.317, R.343, R.346 Ligands: MG.2 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Salt bridges: B:R.343, B:R.343, B:R.343, B:R.346, A:K.222, A:K.222 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 ATP.3: 17 residues within 4Å: Chain B: 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 Chain C: R.307, R.310 Ligands: MG.4 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.188, B:G.229, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, C:R.310 Salt bridges: B:K.232, B:K.232, C:R.307, C:R.307 ATP.6: 19 residues within 4Å: Chain D: D.166, I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, I.348, G.372, A.373, N.376 Chain X: R.291, R.294 Ligands: MG.7 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain X Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:C.210, D:G.211, D:K.212, D:T.213, D:M.214, D:N.376 Salt bridges: D:K.212, D:K.212, X:R.291, X:R.291, X:R.291, X:R.294 ATP.8: 18 residues within 4Å: Chain X: E.134, I.135, G.136, L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, N.280, H.316, G.340 Chain Y: D.318, R.344, R.347 Ligands: MG.9 15 PLIP interactions: 4 interactions with chain Y, 11 interactions with chain X Salt bridges: Y:R.344, Y:R.344, Y:R.344, Y:R.347, X:K.180, X:K.180 Hydrogen bonds: X:G.136, X:G.136, X:G.177, X:T.178, X:G.179, X:K.180, X:T.181, X:L.182, X:N.280

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: 2 residues within 4Å: Chain B: T.233 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.233 MG.7: 2 residues within 4Å: Chain D: T.213 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.213 MG.9: 2 residues within 4Å: Chain X: T.181 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:T.181 MG.11: 3 residues within 4Å: Chain Y: T.234, D.286 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:T.234

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

ADP.5: 12 residues within 4Å: Chain C: G.152, L.154, P.192, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, K.360 9 PLIP interactions: 9 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 Salt bridges: C:K.196 ADP.10: 13 residues within 4Å: Chain A: R.333 Chain Y: I.188, G.189, G.230, T.231, G.232, K.233, T.234, L.235, I.365, H.369, K.397 Ligands: MG.11 11 PLIP interactions: 7 interactions with chain Y, 4 interactions with chain A Hydrogen bonds: Y:G.189, Y:G.230, Y:T.231, Y:T.231, Y:K.233, Y:T.234, A:D.307, A:R.333 Salt bridges: Y:K.233, A:R.333, A:R.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Draczkowski, P. et al., Cryo-EM structure of human 26S proteasomal RP subcomplex bound with branched Ub chain. To Be Published

Release Date

2024-12-18

Peptides

26S protease regulatory subunit 7: A
26S protease regulatory subunit 4: B
26S protease regulatory subunit 8: C
26S protease regulatory subunit 6B: D
Proteasome subunit alpha type-6: E
Proteasome subunit alpha type-2: F
Proteasome subunit alpha type-4: G
Proteasome subunit alpha type-7: H
Proteasome subunit alpha type-5: I
Proteasome subunit alpha type-1: J
Proteasome subunit alpha type-3: K
26S proteasome non-ATPase regulatory subunit 1: L
26S proteasome non-ATPase regulatory subunit 14: M
26S proteasome non-ATPase regulatory subunit 3: N
26S proteasome non-ATPase regulatory subunit 12: O
26S proteasome non-ATPase regulatory subunit 11: P
26S proteasome non-ATPase regulatory subunit 6: Q
26S proteasome non-ATPase regulatory subunit 7: R
26S proteasome non-ATPase regulatory subunit 13: S
26S proteasome non-ATPase regulatory subunit 4: T
26S proteasome non-ATPase regulatory subunit 8: U
26S proteasome complex subunit DSS1: V
26S proteasome non-ATPase regulatory subunit 2: W
26S protease regulatory subunit 10B: X
26S protease regulatory subunit 6A: Y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
G

F
H

G
I

H
J

I
K

J
L

K
M

L
U

M
c

N
V

O
W

P
X

Q
Y

R
Z

S
a

T
b

U
d

V
e

W
f

X
E

Y
F

26S protease regulatory subunit 7

26S protease regulatory subunit 4

26S protease regulatory subunit 8

26S protease 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-5

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 14

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 8

26S proteasome complex subunit DSS1

26S proteasome non-ATPase regulatory subunit 2

26S protease regulatory subunit 10B

26S protease regulatory subunit 6A

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