SMTL ID : 7w3a.1

Structure of USP14-bound human 26S proteasome in substrate-engaged state ED4_USP14

Coordinates

PDB Format

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

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

ADP.1: 14 residues within 4Å: Chain A: 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: G.318 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.178, A:P.218, A:T.220, A:G.221, A:K.222, A:T.223, A:G.382, A:R.386, B:G.318 Salt bridges: A:K.222, A:K.222 ADP.2: 15 residues within 4Å: Chain B: D.186, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, D.285, I.364, H.368, G.392, A.393, K.396 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.188, B:G.188, B:G.229, B:G.229, B:T.230, B:K.232, B:T.233, B:T.233, B:K.396, B:K.396 Salt bridges: B:K.232

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

ATP.3: 17 residues within 4Å: Chain C: M.142, I.143, P.183, P.184, G.185, T.186, G.187, K.188, T.189, L.190, E.242, I.320, H.324, A.349, K.352 Chain D: R.323, R.326 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:I.143, C:P.183, C:G.185, C:T.186, C:G.187, C:K.188, C:T.189, C:T.189, C:L.190, C:E.242, C:K.352 Salt bridges: C:K.188, C:K.188, D:R.323, D:R.323, D:R.323, D:R.326 ATP.4: 17 residues within 4Å: Chain D: I.167, G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, I.348, A.373 Chain E: D.279, R.305, R.308 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain D Salt bridges: E:R.305, E:R.305, E:R.305, E:R.308, D:K.212, D:K.212 Hydrogen bonds: D:G.168, D:G.209, D:C.210, D:G.211, D:K.212, D:T.213, D:T.213 ATP.5: 16 residues within 4Å: Chain E: E.148, I.149, P.190, G.191, T.192, G.193, K.194, T.195, L.196, N.294, I.326, H.330, G.354, A.355 Chain F: R.344, R.347 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.191, E:T.192, E:G.193, E:G.193, E:T.195, E:T.195, E:L.196, E:N.294, E:G.354 Salt bridges: E:K.194, F:R.344, F:R.344, F:R.344, F:R.347 ATP.6: 17 residues within 4Å: Chain A: R.333, R.336 Chain F: D.187, G.189, 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 15 PLIP interactions: 11 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.189, F:G.189, F:G.232, F:K.233, F:T.234, F:T.234, F:T.234, F:N.333 Salt bridges: F:K.233, F:K.233, F:K.233, A:R.333, A:R.333, A:R.333, A:R.336

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain j: H.113, H.115, D.126 3 PLIP interactions: 3 interactions with chain j Metal complexes: j:H.113, j:H.115, j: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: GU
Proteasome subunit alpha type-2: HV
Proteasome subunit alpha type-4: IW
Proteasome subunit alpha type-7: JX
Proteasome subunit alpha type-5: KY
Isoform Long of Proteasome subunit alpha type-1: LZ
Proteasome subunit alpha type-3: M0
Proteasome subunit beta type-6: N1
Proteasome subunit beta type-7: O2
Proteasome subunit beta type-3: P3
Proteasome subunit beta type-2: Q4
Proteasome subunit beta type-5: R5
Proteasome subunit beta type-1: S6
Proteasome subunit beta type-4: T7
Substrate: 8
Ubiquitin carboxyl-terminal hydrolase 14: 9
Ubiquitin: a
26S proteasome non-ATPase regulatory subunit 1: b
26S proteasome non-ATPase regulatory subunit 3: c
26S proteasome non-ATPase regulatory subunit 12: d
26S proteasome non-ATPase regulatory subunit 11: e
26S proteasome non-ATPase regulatory subunit 6: f
26S proteasome non-ATPase regulatory subunit 7: g
26S proteasome non-ATPase regulatory subunit 13: h
26S proteasome non-ATPase regulatory subunit 4: i
26S proteasome non-ATPase regulatory subunit 14: j
26S proteasome non-ATPase regulatory subunit 8: k
26S proteasome non-ATPase regulatory subunit 2: 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

U
g

H
H

V
h

I
I

W
i

J
J

X
j

K
K

Y
k

L
L

Z
l

M
M

0
m

N
N

1
n

O
O

2
o

P
P

3
p

Q
Q

4
q

R
R

5
r

S
S

6
s

T
T

7
t

8
v

9
x

a
y

b
U

c
V

d
W

e
X

f
Y

g
Z

h
a

i
b

j
c

k
d

l
f

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

Substrate

Ubiquitin carboxyl-terminal hydrolase 14

Ubiquitin

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 non-ATPase regulatory subunit 2

26S proteasome complex subunit DSS1

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