SMTL ID : 7w3f.1

Structure of USP14-bound human 26S proteasome in substrate-engaged state ED1_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: 16 residues within 4Å: Chain A: D.176, V.177, P.217, P.218, G.219, T.220, G.221, K.222, T.223, L.224, N.322, I.354, H.358, G.382, A.383 Chain B: R.343 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.219, A:T.220, A:T.220, A:G.221, A:K.222, A:T.223, A:T.223, A:L.224, A:N.322, B:R.343 Salt bridges: A:K.222, A:K.222, B:R.343 ATP.2: 19 residues within 4Å: Chain B: D.186, I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, E.286, N.332, I.364, H.368, G.392, A.393, K.396 Chain C: R.299, R.302 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:G.392 Salt bridges: B:K.232, B:K.232, C:R.299, C:R.299, C:R.299, C:R.302 ATP.3: 17 residues within 4Å: Chain C: M.142, I.143, G.144, P.184, G.185, T.186, G.187, K.188, T.189, L.190, E.242, I.320, H.324, G.348, A.349 Chain D: D.297, R.326 12 PLIP interactions: 4 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:R.326, C:G.144, C:G.187, C:K.188, C:T.189, C:L.190, C:E.242 Salt bridges: D:R.323, D:R.323, D:R.326, C:K.188, C:K.188 ATP.4: 18 residues within 4Å: Chain D: I.167, G.168, P.207, P.208, G.209, C.210, G.211, K.212, T.213, M.214, E.266, I.348, G.372, A.373, N.376 Chain E: D.279, R.305, R.308 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:G.168, D:G.168, D:G.209, D:C.210, D:G.211, D:K.212, D:T.213, D:T.213, D:T.213, D:M.214, D:E.266, D:E.266, D:N.376, E:R.308 Salt bridges: D:K.212, D:K.212, E:R.305, E:R.305, E:R.305

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

ADP.5: 13 residues within 4Å: Chain E: E.148, P.190, G.191, T.192, G.193, K.194, T.195, L.196, I.326, H.330, G.354, A.355, R.358 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.191, E:T.192, E:T.192, E:G.193, E:G.193, E:K.194, E:T.195, E:L.196, E:G.354 Salt bridges: E:K.194

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain 0: H.113, H.115, W.121, V.144 3 PLIP interactions: 3 interactions with chain 0 Metal complexes: 0:H.113, 0:H.115, 0:H.115

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
Substrate: h
Ubiquitin carboxyl-terminal hydrolase 14: i
Ubiquitin: j
26S proteasome non-ATPase regulatory subunit 12: 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
v

i
x

j
y

k
W

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

Substrate

Ubiquitin carboxyl-terminal hydrolase 14

Ubiquitin

26S proteasome non-ATPase regulatory subunit 12

26S proteasome non-ATPase regulatory subunit 3

26S proteasome complex subunit DSS1

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