SMTL ID : 8k0g.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: D.176, G.178, G.219, T.220, G.221, K.222, T.223, L.224, I.354, H.358, G.382, R.386 Chain B: R.343, R.346 Ligands: MG.2 15 PLIP interactions: 4 interactions with chain B, 11 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, A:G.382 ATP.3: 19 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, I.364, H.368, G.392, A.393, K.396 Chain E: R.307, R.310 Ligands: MG.4 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:G.188, B:G.229, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, B:E.286, B:K.396, B:K.396 Salt bridges: B:K.232, B:K.232, E:R.307, E:R.307, E:R.307, E:R.310 ATP.7: 12 residues within 4Å: Chain A: R.333 Chain D: D.187, G.189, P.229, T.231, G.232, K.233, T.234, L.235, I.365, H.369, K.397 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.189, D:G.189, D:T.231, D:G.232, D:K.233, D:T.234, D:T.234 Salt bridges: D:K.233, D:K.233, A:R.333, A:R.333

4 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 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: T.213 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.213 MG.9: 2 residues within 4Å: Chain E: T.197 Ligands: ADP.8 No protein-ligand interaction detected (PLIP)

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

ADP.5: 11 residues within 4Å: Chain C: G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, A.373 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.168, C:G.168, C:G.209, C:G.211, C:K.212, C:T.213, C:T.213, C:M.214 Salt bridges: C:K.212 ADP.8: 15 residues within 4Å: Chain C: R.323 Chain E: M.150, I.151, L.154, G.193, T.194, G.195, K.196, T.197, L.198, I.328, H.332, A.357, K.360 Ligands: MG.9 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.152, E:G.193, E:T.194, E:G.195, E:K.196, E:T.197, E:L.198 Salt bridges: E:K.196, C:R.323, C:R.323

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

2025-01-22

Peptides

26S protease regulatory subunit 7: A
26S protease regulatory subunit 4: B
26S protease regulatory subunit 6B: C
26S protease regulatory subunit 6A: D
26S protease regulatory subunit 8: E
Proteasome subunit alpha type-6: F
Proteasome subunit alpha type-2: G
Proteasome subunit alpha type-4: H
Proteasome subunit alpha type-7: I
Proteasome subunit alpha type-5: J
Proteasome subunit alpha type-1: K
Proteasome subunit alpha type-3: L
26S proteasome non-ATPase regulatory subunit 3: M
26S proteasome non-ATPase regulatory subunit 12: N
26S proteasome non-ATPase regulatory subunit 11: O
26S proteasome non-ATPase regulatory subunit 6: P
26S proteasome non-ATPase regulatory subunit 8: Q
26S proteasome complex subunit DSS1: R
26S proteasome non-ATPase regulatory subunit 2: S
Protein SIC1: T
26S protease regulatory subunit 10B: U
26S proteasome non-ATPase regulatory subunit 1: V
26S proteasome non-ATPase regulatory subunit 7: W
26S proteasome non-ATPase regulatory subunit 13: X
26S proteasome non-ATPase regulatory subunit 4: Y
26S proteasome non-ATPase regulatory subunit 14: Z
Polyubiquitin-B: 0123

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
F

E
C

F
G

G
H

H
I

I
J

J
K

K
L

L
M

M
V

N
W

O
X

P
Y

Q
d

R
e

S
f

T
y

U
E

V
U

W
Z

X
a

Y
b

Z
c

0
u

1
v

2
w

3
x

26S protease regulatory subunit 7

26S protease regulatory subunit 4

26S protease regulatory subunit 6B

26S protease regulatory subunit 6A

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-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

Protein SIC1

26S protease regulatory subunit 10B

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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