SMTL ID : 7w39.1

Structure of USP14-bound human 26S proteasome in state EA2.1_UBL

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.217, 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: R.343, R.346 Ligands: MG.2 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.178, A:G.219, A:T.220, A:G.221, A:K.222, A:T.223, A:L.224 Salt bridges: A:K.222, A:K.222, B:R.343, B:R.343, B:R.343, B:R.346 ATP.3: 17 residues within 4Å: Chain B: I.187, 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: R.299, R.302 Ligands: MG.4 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain B Salt bridges: C:R.299, C:R.299, C:R.302, B:K.232, B:K.232 Hydrogen bonds: B:G.229, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, B:E.286, B:G.392, B:A.393 ATP.6: 18 residues within 4Å: Chain D: G.168, M.170, P.208, G.209, C.210, G.211, K.212, T.213, M.214, N.312, I.344, I.348, G.372, A.373, N.376 Chain E: R.305, R.308 Ligands: MG.7 16 PLIP interactions: 12 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:M.214, D:N.312, D:N.376 Salt bridges: D:K.212, D:K.212, E:R.305, E:R.305, E:R.305, E:R.308 ATP.8: 18 residues within 4Å: Chain E: I.149, G.150, P.190, G.191, T.192, G.193, K.194, T.195, L.196, E.248, N.294, I.326, H.330, G.354, A.355 Chain F: R.344, R.347 Ligands: MG.9 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.150, E:G.150, E:G.191, E:T.192, E:G.193, E:K.194, E:T.195, E:L.196, E:E.248, E:N.294, E:N.294 Salt bridges: E:K.194, E:K.194, F:R.344, F:R.344, F:R.344, F:R.347

5 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: 3 residues within 4Å: Chain B: T.233 Chain C: R.302 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.233 MG.7: 2 residues within 4Å: Chain D: T.213 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.213 MG.9: 4 residues within 4Å: Chain E: T.195, D.247, E.248 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.195 MG.11: 3 residues within 4Å: Chain F: T.234, E.287 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.234

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

ADP.5: 13 residues within 4Å: Chain C: M.142, G.144, L.146, P.184, G.185, T.186, G.187, K.188, T.189, L.190, I.320, G.348, K.352 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.144, C:G.144, C:G.185, C:T.186, C:G.187, C:K.188, C:T.189, C:T.189, C:L.190 Salt bridges: C:K.188 ADP.10: 17 residues within 4Å: Chain A: R.333, R.336 Chain F: D.187, I.188, G.189, P.229, G.230, T.231, G.232, K.233, T.234, L.235, I.365, H.369, G.393, K.397 Ligands: MG.11 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain F Hydrogen bonds: A:R.336, F:G.189, F:G.189, F:P.229, F:T.231, F:T.231, F:G.232, F:K.233, F:T.234, F:T.234 Salt bridges: A:R.333, F:K.233

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 5 residues within 4Å: Chain 2: H.113, H.115, S.123, D.126 Chain k: G.76 3 PLIP interactions: 3 interactions with chain 2 Metal complexes: 2:H.113, 2:H.115, 2: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: G6
Proteasome subunit alpha type-2: H7
Proteasome subunit alpha type-4: I8
Proteasome subunit alpha type-7: J9
Proteasome subunit alpha type-5: Ka
Isoform Long of Proteasome subunit alpha type-1: Lb
Proteasome subunit alpha type-3: Mc
Proteasome subunit beta type-6: Nd
Proteasome subunit beta type-7: Oe
Proteasome subunit beta type-3: Pf
Proteasome subunit beta type-2: Qg
Proteasome subunit beta type-5: Rh
Proteasome subunit beta type-1: Si
Proteasome subunit beta type-4: Tj
26S proteasome non-ATPase regulatory subunit 1: U
26S proteasome non-ATPase regulatory subunit 3: V
26S proteasome non-ATPase regulatory subunit 12: W
26S proteasome non-ATPase regulatory subunit 11: X
26S proteasome non-ATPase regulatory subunit 6: Y
26S proteasome non-ATPase regulatory subunit 7: Z
26S proteasome non-ATPase regulatory subunit 13: 0
26S proteasome non-ATPase regulatory subunit 4: 1
26S proteasome non-ATPase regulatory subunit 14: 2
26S proteasome non-ATPase regulatory subunit 8: 3
26S proteasome complex subunit DSS1: 4
26S proteasome non-ATPase regulatory subunit 2: 5
Ubiquitin: k
Substrate: l
Ubiquitin carboxyl-terminal hydrolase 14: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

6
g

H
H

7
h

I
I

8
i

J
J

9
j

K
K

a
k

L
L

b
l

M
M

c
m

N
N

d
n

O
O

e
o

P
P

f
p

Q
Q

g
q

R
R

h
r

S
S

i
s

T
T

j
t

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

k
u

l
v

m
x

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 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 complex subunit DSS1

26S proteasome non-ATPase regulatory subunit 2

Ubiquitin

Substrate

Ubiquitin carboxyl-terminal hydrolase 14

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