SMTL ID : 7w3h.1

Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.1_USP14

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: D.176, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, I.354, H.358, G.382, A.383, R.386 Chain B: D.317, R.343, R.346 Ligands: MG.2 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.178, A:G.219, A:T.220, A:T.220, A:T.220, A:G.221, A:K.222, A:T.223, A:L.224, A:G.382, A:R.386 Salt bridges: A:K.222, A:K.222, B:R.343, B:R.343, B:R.343, B:R.346 ATP.3: 18 residues within 4Å: Chain B: G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, E.286, N.332, I.364, H.368, G.392, K.396 Chain C: R.299, R.302 Ligands: MG.4 17 PLIP interactions: 13 interactions with chain B, 4 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:T.233, B:L.234, B:N.332, B:N.332, B:K.396 Salt bridges: B:K.232, B:K.232, C:R.299, C:R.299, C:R.299, C:R.302 ATP.5: 20 residues within 4Å: Chain C: M.142, I.143, G.144, L.146, P.184, G.185, T.186, G.187, K.188, T.189, L.190, R.193, I.320, H.324, G.348, A.349, K.352 Chain D: R.323, R.326 Ligands: MG.6 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.144, C:G.185, C:T.186, C:T.186, C:G.187, C:K.188, C:T.189, C:T.189, C:T.189, C:L.190, C:R.193 Salt bridges: D:R.323, D:R.323, D:R.323, D:R.326 ATP.8: 21 residues within 4Å: Chain A: D.307, R.333, R.336 Chain F: D.187, I.188, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, G.393, A.394, K.397 Ligands: MG.9 15 PLIP interactions: 11 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.189, F:G.189, F:T.231, F:T.231, F:G.232, F:K.233, F:T.234, F:L.235, F:N.333 Salt bridges: F:K.233, F:K.233, A:R.333, A:R.333, A:R.333, A:R.336

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 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.233 MG.6: 2 residues within 4Å: Chain C: T.189 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: R.333 Chain F: T.234 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.234

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

ADP.7: 13 residues within 4Å: Chain D: G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, G.372, A.373, N.376 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:G.211, D:K.212, D:T.213, D:M.214, D:N.376 Salt bridges: D:K.212, D:K.212

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain 1: H.113, H.115, W.121, S.123, D.126 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:H.113, 1:H.115, 1:H.115, 1:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., USP14-regulated allostery of the human proteasome by time-resolved cryo-EM. Nature (2022)

Release Date

2022-05-04

Peptides

26S protease regulatory subunit 7: A
26S protease regulatory subunit 4: B
Isoform 2 of 26S proteasome regulatory subunit 8: C
26S protease regulatory subunit 6B: D
26S proteasome regulatory subunit 10B: E
26S protease regulatory subunit 6A: F
Proteasome subunit alpha type-6: G4
Proteasome subunit alpha type-2: H5
Proteasome subunit alpha type-4: I6
Proteasome subunit alpha type-7: J7
Proteasome subunit alpha type-5: K8
Isoform Long of Proteasome subunit alpha type-1: L9
Proteasome subunit alpha type-3: Ma
Proteasome subunit beta type-6: Nb
Proteasome subunit beta type-7: Oc
Proteasome subunit beta type-3: Pd
Proteasome subunit beta type-2: Qe
Proteasome subunit beta type-5: Rf
Proteasome subunit beta type-1: Sg
Proteasome subunit beta type-4: Th
26S proteasome non-ATPase regulatory subunit 1: U
26S proteasome non-ATPase regulatory subunit 3: V
26S proteasome non-ATPase regulatory subunit 11: W
26S proteasome non-ATPase regulatory subunit 6: X
26S proteasome non-ATPase regulatory subunit 7: Y
26S proteasome non-ATPase regulatory subunit 13: Z
26S proteasome non-ATPase regulatory subunit 4: 0
26S proteasome non-ATPase regulatory subunit 14: 1
26S proteasome non-ATPase regulatory subunit 8: 2
26S proteasome non-ATPase regulatory subunit 2: 3
Substrate: i
Ubiquitin carboxyl-terminal hydrolase 14: j
Ubiquitin: k
26S proteasome non-ATPase regulatory subunit 12: l
26S proteasome complex subunit DSS1: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

4
g

H
H

5
h

I
I

6
i

J
J

7
j

K
K

8
k

L
L

9
l

M
M

a
m

N
N

b
n

O
O

c
o

P
P

d
p

Q
Q

e
q

R
R

f
r

S
S

g
s

T
T

h
t

U
U

V
V

W
X

X
Y

Y
Z

Z
a

0
b

1
c

2
d

3
f

i
v

j
x

k
y

l
W

m
e

26S protease regulatory subunit 7

26S protease regulatory subunit 4

Isoform 2 of 26S proteasome regulatory subunit 8

26S protease regulatory subunit 6B

26S proteasome 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

Isoform Long of 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

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 3

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 non-ATPase regulatory subunit 2

Substrate

Ubiquitin carboxyl-terminal hydrolase 14

Ubiquitin

26S proteasome non-ATPase regulatory subunit 12

26S proteasome complex subunit DSS1

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