SMTL ID : 8jti.1

Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-4-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: D.176, V.177, G.178, G.219, T.220, G.221, K.222, T.223, L.224, N.322, H.358, G.382, A.383 Chain B: R.343, R.346 Ligands: MG.2 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:V.177, A:G.219, A:G.221, A:K.222, A:T.223, A:L.224, A:N.322, B:D.317 Salt bridges: A:K.222, A:K.222, B:R.343, B:R.343, B:R.343, B:R.346 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 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C 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, C:R.310 Salt bridges: B:K.232, B:K.232, C:R.307, C:R.307 ATP.6: 18 residues within 4Å: Chain D: D.166, I.167, G.168, M.170, G.209, C.210, G.211, K.212, T.213, M.214, I.344, G.372, A.373, N.376 Chain E: D.265, R.291, R.294 Ligands: MG.7 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:C.210, D:G.211, D:K.212, D:T.213, D:T.213, D:M.214, D:N.376 Salt bridges: D:K.212, D:K.212, E:R.291, E:R.291, E:R.291, E:R.294 ATP.8: 14 residues within 4Å: Chain E: E.134, G.136, L.138, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316 Chain F: R.344, R.347 Ligands: MG.9 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.136, E:G.136, E:G.177, E:G.179, E:K.180, E:T.181, E:L.182 Salt bridges: E:K.180, E:K.180, F:R.344, F: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: 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 E: T.181 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.181 MG.11: 3 residues within 4Å: Chain F: T.234, D.286 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.234

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

ADP.5: 12 residues within 4Å: Chain C: M.150, G.152, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, G.356, A.357 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.152, C:G.193, C:T.194, C:G.195, C:K.196, C:K.196, C:T.197, C:L.198 ADP.10: 14 residues within 4Å: Chain A: R.333 Chain F: I.188, G.189, P.229, G.230, T.231, G.232, K.233, T.234, L.235, I.365, H.369, K.397 Ligands: MG.11 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:G.189, F:G.189, F:K.233, F:T.234, F:L.235 Salt bridges: F:K.233, F: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

2024-12-25

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
26S protease regulatory subunit 10B: E
26S protease 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 8: T
26S proteasome complex subunit DSS1: U
26S proteasome non-ATPase regulatory subunit 2: 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: Z012

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
d

U
e

V
f

W
a

X
b

Y
c

Z
v

0
u

1
x

2
w

26S protease regulatory subunit 7

26S protease regulatory subunit 4

26S protease regulatory subunit 8

26S protease regulatory subunit 6B

26S protease regulatory subunit 10B

26S protease 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 8

26S proteasome complex subunit DSS1

26S proteasome non-ATPase regulatory subunit 2

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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