SMTL ID : 5vfq.1

Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain W: H.90, S.91, H.92 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:S.91, W:H.92, W:H.92

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 20 residues within 4Å: Chain d: D.142, V.143, G.144, P.184, G.185, T.186, G.187, K.188, T.189, L.190, N.288, I.320, H.324, G.348, A.349, R.352 Chain e: D.266, A.289, R.292, R.295 14 PLIP interactions: 9 interactions with chain d, 5 interactions with chain e Hydrogen bonds: d:G.144, d:G.185, d:T.186, d:G.187, d:K.188, d:T.189, d:T.189, d:G.348, d:R.352, e:D.266, e:R.292 Salt bridges: e:R.292, e:R.292, e:R.295 AGS.3: 15 residues within 4Å: Chain f: M.140, I.141, G.142, G.183, T.184, G.185, K.186, T.187, L.188, I.318, H.322, G.346, A.347 Chain g: D.259, R.288 9 PLIP interactions: 1 interactions with chain g, 8 interactions with chain f Salt bridges: g:R.288 Hydrogen bonds: f:G.142, f:G.183, f:G.185, f:K.186, f:T.187, f:T.187, f:T.187, f:L.188 AGS.4: 13 residues within 4Å: Chain g: G.130, M.132, P.170, G.171, C.172, G.173, K.174, T.175, M.176, I.306, G.334, A.335, N.338 6 PLIP interactions: 6 interactions with chain g Hydrogen bonds: g:G.130, g:G.130, g:T.175, g:T.175, g:M.176, g:N.338 AGS.5: 17 residues within 4Å: Chain d: R.299, R.302 Chain i: D.144, I.145, G.146, P.186, G.187, T.188, G.189, K.190, T.191, L.192, N.290, I.322, H.326, G.350, A.351 10 PLIP interactions: 7 interactions with chain i, 3 interactions with chain d Hydrogen bonds: i:G.146, i:G.146, i:K.190, i:K.190, i:T.191, i:D.243, i:N.290, d:R.299 Salt bridges: d:R.299, d:R.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Y. et al., Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome. Nat Commun (2018)

Release Date

2018-07-18

Peptides

Proteasome subunit alpha type-6: AZ
Proteasome subunit alpha type-2: B0
Proteasome subunit alpha type-4: C1
Proteasome subunit alpha type-7: D2
Proteasome subunit alpha type-5: E3
Proteasome subunit alpha type-1: F4
Proteasome subunit alpha type-3: G5
Proteasome subunit beta type-6: H6
Proteasome subunit beta type-7: I7
Proteasome subunit beta type-3: J8
Proteasome subunit beta type-2: K9
Proteasome subunit beta type-5: La
Proteasome subunit beta type-1: Mb
Proteasome subunit beta type-4: Nc
26S proteasome non-ATPase regulatory subunit 1: O
26S proteasome non-ATPase regulatory subunit 3: P
26S proteasome non-ATPase regulatory subunit 12: Q
26S proteasome non-ATPase regulatory subunit 11: R
26S proteasome non-ATPase regulatory subunit 6: S
26S proteasome non-ATPase regulatory subunit 7: T
26S proteasome non-ATPase regulatory subunit 13: U
26S proteasome non-ATPase regulatory subunit 4: V
26S proteasome non-ATPase regulatory subunit 14: W
26S proteasome non-ATPase regulatory subunit 8: X
Sem1: Y
26S proteasome regulatory subunit 7: d
26S proteasome regulatory subunit 4: e
26S proteasome regulatory subunit 8: f
26S proteasome regulatory subunit 6B: g
26S proteasome regulatory subunit 10B: h
26S proteasome regulatory subunit 6A: i
26S proteasome non-ATPase regulatory subunit 2: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

Z
g

B
H

0
h

C
I

1
i

D
J

2
j

E
K

3
k

F
L

4
l

G
M

5
m

H
N

6
n

I
O

7
o

J
P

8
p

K
Q

9
q

L
R

a
r

M
S

b
s

N
T

c
t

O
U

P
V

Q
W

R
X

S
Y

T
Z

U
a

V
b

W
c

X
d

Y
e

d
A

e
B

f
C

g
D

h
E

i
F

j
f

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

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

Sem1

26S proteasome regulatory subunit 7

26S proteasome regulatory subunit 4

26S proteasome regulatory subunit 8

26S proteasome regulatory subunit 6B

26S proteasome regulatory subunit 10B

26S proteasome regulatory subunit 6A

26S proteasome non-ATPase regulatory subunit 2

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