SMTL ID : 7w3g.1

Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.0_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: 19 residues within 4Å: Chain A: D.176, V.177, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, R.227, N.322, I.354, H.358, G.382, A.383, R.386 Chain B: R.343, R.346 18 PLIP interactions: 4 interactions with chain B, 14 interactions with chain A Salt bridges: B:R.343, B:R.343, B:R.343, B:R.346, A:K.222, A:K.222, A:R.227 Hydrogen bonds: A:G.178, A:G.219, A:T.220, A:G.221, A:K.222, A:T.223, A:T.223, A:T.223, A:L.224, A:R.227, A:R.386 ATP.2: 19 residues within 4Å: Chain B: E.182, G.188, L.190, P.228, G.229, T.230, G.231, K.232, T.233, L.234, E.286, I.364, H.368, G.392, A.393, K.396 Chain C: D.273, R.299, R.302 16 PLIP interactions: 4 interactions with chain C, 12 interactions with chain B Salt bridges: C:R.299, C:R.299, C:R.299, C:R.302, B:K.232 Hydrogen bonds: B:G.188, B:G.229, B:T.230, B:T.230, B:G.231, B:K.232, B:T.233, B:T.233, B:L.234, B:E.286, B:E.286 ATP.3: 17 residues within 4Å: Chain C: M.142, I.143, 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 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.185, C:T.186, C:G.187, C:K.188, C:T.189, C:T.189, C:R.193 Salt bridges: C:K.188, C:K.188, D:R.323, D:R.323, D:R.323, D:R.326 ATP.5: 15 residues within 4Å: Chain A: R.333 Chain F: D.187, P.229, T.231, G.232, K.233, T.234, L.235, D.286, N.333, I.365, H.369, G.393, A.394, K.397 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain F Salt bridges: A:R.333, A:R.333, A:R.333 Hydrogen bonds: F:T.231, F:T.231, F:T.231, F:G.232, F:K.233, F:T.234, F:T.234, F:L.235, F:G.393

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

ADP.4: 16 residues within 4Å: Chain D: D.166, G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, I.344, I.348, G.372, A.373, N.376 Chain E: R.305 8 PLIP interactions: 8 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

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain 0: H.113, H.115, S.123, D.126 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:H.113, 0:H.115, 0:D.126, 0: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: G3
Proteasome subunit alpha type-2: H4
Proteasome subunit alpha type-4: I5
Proteasome subunit alpha type-7: J6
Proteasome subunit alpha type-5: K7
Isoform Long of Proteasome subunit alpha type-1: L8
Proteasome subunit alpha type-3: M9
Proteasome subunit beta type-6: Na
Proteasome subunit beta type-7: Ob
Proteasome subunit beta type-3: Pc
Proteasome subunit beta type-2: Qd
Proteasome subunit beta type-5: Re
Proteasome subunit beta type-1: Sf
Proteasome subunit beta type-4: Tg
26S proteasome non-ATPase regulatory subunit 1: U
26S proteasome non-ATPase regulatory subunit 11: V
26S proteasome non-ATPase regulatory subunit 6: W
26S proteasome non-ATPase regulatory subunit 7: X
26S proteasome non-ATPase regulatory subunit 13: Y
26S proteasome non-ATPase regulatory subunit 4: Z
26S proteasome non-ATPase regulatory subunit 14: 0
26S proteasome non-ATPase regulatory subunit 8: 1
26S proteasome non-ATPase regulatory subunit 2: 2
Ubiquitin carboxyl-terminal hydrolase 14: h
Ubiquitin: i
26S proteasome non-ATPase regulatory subunit 12: j
Substrate: k
26S proteasome non-ATPase regulatory subunit 3: 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

3
g

H
H

4
h

I
I

5
i

J
J

6
j

K
K

7
k

L
L

8
l

M
M

9
m

N
N

a
n

O
O

b
o

P
P

c
p

Q
Q

d
q

R
R

e
r

S
S

f
s

T
T

g
t

U
U

V
X

W
Y

X
Z

Y
a

Z
b

0
c

1
d

2
f

h
x

i
y

j
W

k
v

l
V

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 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

Ubiquitin carboxyl-terminal hydrolase 14

Ubiquitin

26S proteasome non-ATPase regulatory subunit 12

Substrate

26S proteasome non-ATPase regulatory subunit 3

26S proteasome complex subunit DSS1

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