SMTL ID : 7w3j.1

Structure of USP14-bound human 26S proteasome in substrate-inhibited state SC_USP14

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: I.149, G.150, L.152, P.190, G.191, T.192, G.193, K.194, T.195, L.196, N.294, I.326, H.330, G.354, A.355, R.358 Chain B: R.344, R.347 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.150, A:G.191, A:G.193, A:K.194, A:T.195, A:L.196, A:N.294, A:N.294, A:R.358 Salt bridges: A:K.194, A:K.194, B:R.344, B:R.344, B:R.344, B:R.347 ATP.2: 18 residues within 4Å: Chain 6: R.333, R.336 Chain B: D.187, I.188, G.189, P.228, P.229, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, G.393, A.394, K.397 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain 6 Hydrogen bonds: B:G.189, B:G.189, B:T.231, B:G.232, B:K.233, B:T.234, B:T.234, B:T.234, B:L.235, B:N.333 Salt bridges: B:K.233, B:K.233, 6:R.333, 6:R.333, 6:R.333, 6:R.336 ATP.3: 18 residues within 4Å: Chain 6: D.176, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, I.354, H.358, G.382, A.383, R.386 Chain 7: D.317, R.343, R.346 16 PLIP interactions: 11 interactions with chain 6, 5 interactions with chain 7 Hydrogen bonds: 6:P.218, 6:T.220, 6:T.220, 6:G.221, 6:K.222, 6:T.223, 6:T.223, 6:L.224, 6:E.276, 6:G.382, 6:A.383, 7:D.317, 7:R.346, 7:R.346 Salt bridges: 7:R.343, 7:R.346 ATP.6: 16 residues within 4Å: Chain 9: I.167, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, E.266, I.344, G.372, A.373, N.376 Chain A: R.305, R.308 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain 9 Salt bridges: A:R.305, A:R.305, A:R.305, A:R.308 Hydrogen bonds: 9:G.209, 9:C.210, 9:C.210, 9:G.211, 9:K.212, 9:T.213, 9:T.213, 9:M.214, 9:E.266, 9:N.376

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

ADP.4: 14 residues within 4Å: Chain 7: I.187, G.188, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393 Chain 8: R.299, R.302 14 PLIP interactions: 3 interactions with chain 8, 11 interactions with chain 7 Salt bridges: 8:R.299, 8:R.299, 8:R.302, 7:K.232, 7:K.232 Hydrogen bonds: 7:G.188, 7:G.229, 7:T.230, 7:G.231, 7:K.232, 7:T.233, 7:T.233, 7:L.234, 7:G.392 ADP.5: 13 residues within 4Å: Chain 8: M.142, I.143, L.146, P.184, G.185, T.186, G.187, K.188, T.189, L.190, H.324, A.349, K.352 7 PLIP interactions: 7 interactions with chain 8 Hydrogen bonds: 8:G.144, 8:G.185, 8:T.186, 8:G.187, 8:K.188, 8:T.189, 8:L.190

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain h: H.113, H.115, D.126 4 PLIP interactions: 4 interactions with chain h Metal complexes: h:H.113, h:H.115, h:D.126, h: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 proteasome regulatory subunit 10B: A
26S protease regulatory subunit 6A: B
Proteasome subunit alpha type-6: CQ
Proteasome subunit alpha type-2: DR
Proteasome subunit alpha type-4: ES
Proteasome subunit alpha type-7: FT
Proteasome subunit alpha type-5: GU
Isoform Long of Proteasome subunit alpha type-1: HV
Proteasome subunit alpha type-3: IW
Proteasome subunit beta type-6: JX
Proteasome subunit beta type-7: KY
Proteasome subunit beta type-3: LZ
Proteasome subunit beta type-2: M0
Proteasome subunit beta type-5: N1
Proteasome subunit beta type-1: O2
Proteasome subunit beta type-4: P3
Ubiquitin carboxyl-terminal hydrolase 14: 4
Ubiquitin: 5
26S protease regulatory subunit 7: 6
26S protease regulatory subunit 4: 7
Isoform 2 of 26S proteasome regulatory subunit 8: 8
26S protease regulatory subunit 6B: 9
26S proteasome non-ATPase regulatory subunit 1: a
26S proteasome non-ATPase regulatory subunit 12: b
26S proteasome non-ATPase regulatory subunit 11: c
26S proteasome non-ATPase regulatory subunit 6: d
26S proteasome non-ATPase regulatory subunit 7: e
26S proteasome non-ATPase regulatory subunit 13: f
26S proteasome non-ATPase regulatory subunit 4: g
26S proteasome non-ATPase regulatory subunit 14: h
26S proteasome non-ATPase regulatory subunit 8: i
26S proteasome non-ATPase regulatory subunit 2: j
26S proteasome non-ATPase regulatory subunit 3: k
26S proteasome complex subunit DSS1: l

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

Q
g

D
H

R
h

E
I

S
i

F
J

T
j

G
K

U
k

H
L

V
l

I
M

W
m

J
N

X
n

K
O

Y
o

L
P

Z
p

M
Q

0
q

N
R

1
r

O
S

2
s

P
T

3
t

4
x

5
y

6
A

7
B

8
C

9
D

a
U

b
W

c
X

d
Y

e
Z

f
a

g
b

h
c

i
d

j
f

k
V

l
e

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

Ubiquitin carboxyl-terminal hydrolase 14

Ubiquitin

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 non-ATPase regulatory subunit 1

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 non-ATPase regulatory subunit 2

26S proteasome non-ATPase regulatory subunit 3

26S proteasome complex subunit DSS1

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