SMTL ID : 6wjd.1

SA-like state of human 26S Proteasome with non-cleavable M1-linked hexaubiquitin and E3 ubiquitin ligase E6AP/UBE3A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain I: E.51, H.112, H.114, D.125 Chain S: G.76 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.51, I:H.112, I:H.114, I:H.114, I:D.125

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 14 residues within 4Å: Chain M: D.176, G.178, G.219, T.220, G.221, K.222, T.223, L.224, E.276, I.354, H.358, G.382, A.383 Ligands: MG.3 8 PLIP interactions: 8 interactions with chain M Hydrogen bonds: M:G.178, M:G.221, M:K.222, M:T.223, M:L.224, M:E.276, M:G.382, M:A.383 AGS.4: 12 residues within 4Å: Chain N: I.187, P.227, P.228, G.229, T.230, G.231, K.232, T.233, L.234, G.392, A.393 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain N Hydrogen bonds: N:P.227, N:G.229, N:T.230, N:T.230, N:G.231, N:K.232, N:T.233, N:L.234 AGS.7: 16 residues within 4Å: Chain P: I.167, P.207, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, G.372, A.373, N.376 Chain Q: A.302 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain P Hydrogen bonds: P:G.209, P:C.210, P:G.211, P:K.212, P:T.213, P:M.214, P:N.312, P:N.376 AGS.9: 12 residues within 4Å: Chain Q: G.150, G.191, T.192, G.193, K.194, T.195, L.196, N.294, I.326, G.354, A.355 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain Q Hydrogen bonds: Q:G.150, Q:T.192, Q:G.193, Q:K.194, Q:K.194, Q:T.195, Q:T.195, Q:L.196, Q:N.294, Q:G.354, Q:A.355 Salt bridges: Q:K.194

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain M: T.223, E.276 Ligands: AGS.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain N: T.233 Ligands: AGS.4 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain P: T.213 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.213 MG.10: 2 residues within 4Å: Chain Q: T.195 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.195 MG.12: 4 residues within 4Å: Chain R: T.234, D.286, E.287 Ligands: ADP.11 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:T.234, R:D.286

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

ADP.6: 12 residues within 4Å: Chain O: M.142, G.144, L.146, G.185, T.186, G.187, K.188, T.189, L.190, H.324, G.348, K.352 8 PLIP interactions: 8 interactions with chain O Hydrogen bonds: O:G.144, O:G.185, O:T.186, O:T.186, O:G.187, O:K.188, O:T.189, O:L.190 ADP.11: 13 residues within 4Å: Chain M: R.336 Chain R: G.189, G.230, T.231, G.232, K.233, T.234, L.235, H.369, G.393, A.394, K.397 Ligands: MG.12 11 PLIP interactions: 10 interactions with chain R, 1 interactions with chain M Hydrogen bonds: R:G.189, R:G.189, R:G.230, R:T.231, R:G.232, R:K.233, R:T.234, R:T.234, R:L.235, R:G.393, M:R.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at hRpn11 of the 26S Proteasome. Structure (2020)

Release Date

2020-08-05

Peptides

26S proteasome non-ATPase regulatory subunit 1: A
26S proteasome non-ATPase regulatory subunit 3: B
26S proteasome non-ATPase regulatory subunit 12: C
26S proteasome non-ATPase regulatory subunit 11: D
26S proteasome non-ATPase regulatory subunit 6: E
26S proteasome non-ATPase regulatory subunit 7: F
26S proteasome non-ATPase regulatory subunit 13: G
26S proteasome non-ATPase regulatory subunit 4: H
26S proteasome non-ATPase regulatory subunit 14: I
26S proteasome non-ATPase regulatory subunit 8: J
26S proteasome complex subunit SEM1: K
26S proteasome non-ATPase regulatory subunit 2: L
26S proteasome regulatory subunit 7: M
26S proteasome regulatory subunit 4: N
26S proteasome regulatory subunit 8: O
26S proteasome regulatory subunit 6B: P
26S proteasome regulatory subunit 10B: Q
26S proteasome regulatory subunit 6A: R
Ubiquitin: S
Proteasome subunit alpha type-6: T7
Proteasome subunit alpha type-2: U8
Proteasome subunit alpha type-4: V9
Proteasome subunit alpha type-7: Wa
Proteasome subunit alpha type-5: Xb
Proteasome subunit alpha type-1: Yc
Proteasome subunit alpha type-3: Zd
Proteasome subunit beta type-6: 0e
Proteasome subunit beta type-7: 1f
Proteasome subunit beta type-3: 2g
Proteasome subunit beta type-2: 3h
Proteasome subunit beta type-5: 4i
Proteasome subunit beta type-1: 5j
Proteasome subunit beta type-4: 6k

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
V

C
W

D
X

E
Y

F
Z

G
a

H
b

I
c

J
d

K
e

L
f

M
A

N
B

O
C

P
D

Q
E

R
F

S
u

T
G

7
g

U
H

8
h

V
I

9
i

W
J

a
j

X
K

b
k

Y
L

c
l

Z
M

d
m

0
N

e
n

1
O

f
o

2
P

g
p

3
Q

h
q

4
R

i
r

5
S

j
s

6
T

k
t

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 13

26S proteasome non-ATPase regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 14

26S proteasome non-ATPase regulatory subunit 8

26S proteasome complex subunit SEM1

26S proteasome non-ATPase regulatory subunit 2

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 8

26S proteasome regulatory subunit 6B

26S proteasome regulatory subunit 10B

26S proteasome regulatory subunit 6A

Ubiquitin

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

Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-5

Proteasome subunit beta type-1

Proteasome subunit beta type-4

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