SMTL ID : 7w38.1

Structure of USP14-bound human 26S proteasome in state EA2.0_UBL

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 20 residues within 4Å: Chain A: D.176, V.177, G.178, 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: D.317, R.343, R.346 Ligands: MG.2 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:V.177, A:G.178, A:G.219, A:T.220, A:G.221, A:K.222, A:T.223, A:T.223, A:L.224, B:D.317 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, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 Chain C: R.299, R.302 Ligands: MG.4 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.188, B:G.229, B:T.230, B:T.230, B:G.231, B:K.232, B:T.233, B:L.234, C:R.302 Salt bridges: B:K.232, B:K.232, C:R.299, C:R.299 ATP.7: 19 residues within 4Å: Chain D: I.167, G.168, M.170, P.207, 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, R.308 Ligands: MG.8 14 PLIP interactions: 11 interactions with chain D, 3 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:M.214 Salt bridges: D:K.212, D:K.212, E:R.305, E:R.305, E:R.308 ATP.9: 20 residues within 4Å: Chain E: E.148, I.149, G.150, P.189, 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 Ligands: MG.10 Chain j: R.344, R.347 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain j Hydrogen bonds: E:G.150, E:G.150, E:G.191, E:T.192, E:G.193, E:K.194, E:T.195, E:T.195, E:L.196, E:N.294, E:N.294 Salt bridges: E:K.194, E:K.194, j:R.344, j:R.344, j:R.344, j:R.347

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

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, D.285 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.233 MG.6: 1 residues within 4Å: Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: T.213 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.213 MG.10: 4 residues within 4Å: Chain E: T.195, D.247, E.248 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.195 MG.13: 3 residues within 4Å: Ligands: ADP.12 Chain j: T.234, D.286 1 PLIP interactions: 1 interactions with chain j Metal complexes: j:T.234

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

ADP.5: 14 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 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.144, C:P.183, C:G.185, C:T.186, C:T.186, C:G.187, C:K.188, C:T.189, C:T.189, C:L.190 Salt bridges: C:K.188 ADP.12: 16 residues within 4Å: Chain A: R.333 Ligands: MG.13 Chain j: D.187, G.189, P.229, G.230, T.231, G.232, K.233, T.234, L.235, E.287, I.365, H.369, G.393, K.397 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain j Salt bridges: A:R.333, A:R.333, j:K.233, j:K.233 Hydrogen bonds: j:G.189, j:G.189, j:G.232, j:K.233, j:T.234

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain i: H.113, H.115, D.126 Chain k: G.76 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:H.113, i:H.115, i:D.126, i: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
Proteasome subunit alpha type-6: F3
Proteasome subunit alpha type-2: G4
Proteasome subunit alpha type-4: H5
Proteasome subunit alpha type-7: I6
Proteasome subunit alpha type-5: J7
Isoform Long of Proteasome subunit alpha type-1: K8
Proteasome subunit alpha type-3: L9
Proteasome subunit beta type-6: Ma
Proteasome subunit beta type-7: Nb
Proteasome subunit beta type-3: Oc
Proteasome subunit beta type-2: Pd
Proteasome subunit beta type-5: Qe
Proteasome subunit beta type-1: Rf
Proteasome subunit beta type-4: Sg
26S proteasome non-ATPase regulatory subunit 1: T
26S proteasome non-ATPase regulatory subunit 3: U
26S proteasome non-ATPase regulatory subunit 12: V
26S proteasome non-ATPase regulatory subunit 11: W
26S proteasome non-ATPase regulatory subunit 6: X
26S proteasome non-ATPase regulatory subunit 7: Y
26S proteasome non-ATPase regulatory subunit 13: Z
26S proteasome non-ATPase regulatory subunit 4: 0
26S proteasome non-ATPase regulatory subunit 8: 1
26S proteasome non-ATPase regulatory subunit 2: 2
Ubiquitin carboxyl-terminal hydrolase 14: h
26S proteasome non-ATPase regulatory subunit 14: i
26S protease regulatory subunit 6A: j
Ubiquitin: k
26S proteasome complex subunit DSS1: l

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

3
g

G
H

4
h

H
I

5
i

I
J

6
j

J
K

7
k

K
L

8
l

L
M

9
m

M
N

a
n

N
O

b
o

O
P

c
p

P
Q

d
q

Q
R

e
r

R
S

f
s

S
T

g
t

T
U

U
V

V
W

W
X

X
Y

Y
Z

Z
a

0
b

1
d

2
f

h
x

i
c

j
F

k
u

l
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

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 8

26S proteasome non-ATPase regulatory subunit 2

Ubiquitin carboxyl-terminal hydrolase 14

26S proteasome non-ATPase regulatory subunit 14

26S protease regulatory subunit 6A

Ubiquitin

26S proteasome complex subunit DSS1

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