SMTL ID : 8jrt.1

Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-3-mer

Ligands

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

ATP.1: 17 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, H.358, G.382, A.383 Chain B: D.317, R.343, R.346 Ligands: MG.2 13 PLIP interactions: 4 interactions with chain B, 9 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.219, A:T.220, A:G.221, A:K.222, A:T.223, A:L.224 ATP.3: 16 residues within 4Å: Chain B: I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, 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: 17 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, G.372, A.373, N.376 Chain S: D.265, R.291, R.294 Ligands: MG.7 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain S 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, S:R.291, S:R.291, S:R.291, S:R.294 ATP.8: 16 residues within 4Å: Chain S: G.136, L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, N.280, I.312, H.316, G.340 Chain T: R.344, R.347 Ligands: MG.9 15 PLIP interactions: 11 interactions with chain S, 4 interactions with chain T Hydrogen bonds: S:G.136, S:G.136, S:G.177, S:G.179, S:G.179, S:K.180, S:T.181, S:L.182, S:N.280 Salt bridges: S:K.180, S:K.180, T:R.344, T:R.344, T:R.344, T:R.347

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.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: 3 residues within 4Å: Chain S: T.181, D.233 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.181 MG.11: 3 residues within 4Å: Chain T: T.234, D.286 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.234

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

ADP.5: 15 residues within 4Å: Chain C: M.150, 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 7 PLIP interactions: 7 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 ADP.10: 13 residues within 4Å: Chain A: R.333 Chain T: 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: 9 interactions with chain T, 2 interactions with chain A Hydrogen bonds: T:G.189, T:G.189, T:G.230, T:T.231, T:K.233, T:T.234, T:L.235, T:K.397 Salt bridges: T: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 3: L
26S proteasome non-ATPase regulatory subunit 12: M
26S proteasome non-ATPase regulatory subunit 11: N
26S proteasome non-ATPase regulatory subunit 6: O
26S proteasome non-ATPase regulatory subunit 8: P
26S proteasome complex subunit DSS1: Q
26S proteasome non-ATPase regulatory subunit 2: R
26S protease regulatory subunit 10B: S
26S protease regulatory subunit 6A: T
26S proteasome non-ATPase regulatory subunit 1: U
26S proteasome non-ATPase regulatory subunit 7: V
26S proteasome non-ATPase regulatory subunit 13: W
26S proteasome non-ATPase regulatory subunit 4: X
26S proteasome non-ATPase regulatory subunit 14: Y
Polyubiquitin-B: Z01

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
V

M
W

N
X

O
Y

P
d

Q
e

R
f

S
E

T
F

U
U

V
Z

W
a

X
b

Y
c

Z
v

0
u

1
w

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 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 8

26S proteasome complex subunit DSS1

26S proteasome non-ATPase regulatory subunit 2

26S protease regulatory subunit 10B

26S protease regulatory subunit 6A

26S proteasome non-ATPase regulatory subunit 1

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

Polyubiquitin-B

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