SMTL ID : 5vfr.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-1-1-1-1-1-1-1-1-1-1-1-2-2-2-2-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain I: V.30, H.90, S.91, H.92 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:V.30, I:S.91

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

AGS.2: 15 residues within 4Å: Chain d: G.145, C.146, P.184, G.185, T.186, G.187, K.188, T.189, L.190, D.241, I.320, I.323, H.324, G.348, A.349 10 PLIP interactions: 10 interactions with chain d Hydrogen bonds: d:C.146, d:G.185, d:T.186, d:T.186, d:G.187, d:K.188, d:T.189, d:T.189, d:T.189, d:G.348 AGS.3: 15 residues within 4Å: Chain e: D.135, G.138, P.177, G.178, T.179, G.180, K.181, T.182, L.183, E.235, N.281, H.317, G.341, A.342 Chain f: R.297 12 PLIP interactions: 12 interactions with chain e Hydrogen bonds: e:D.135, e:D.135, e:G.178, e:T.179, e:G.180, e:K.181, e:T.182, e:T.182, e:N.281, e:N.281, e:N.281, e:G.341 AGS.4: 16 residues within 4Å: Chain g: G.130, P.170, G.171, G.173, K.174, T.175, M.176, K.179, I.306, I.310, G.334, A.335, N.338 Chain h: D.251, R.277, R.280 14 PLIP interactions: 11 interactions with chain g, 3 interactions with chain h Hydrogen bonds: g:G.130, g:G.171, g:G.173, g:K.174, g:T.175, g:T.175, g:T.175, g:M.176, g:K.179, g:N.338, h:R.277 Salt bridges: g:K.179, h:R.277, h:R.277 AGS.5: 14 residues within 4Å: Chain i: P.186, G.187, T.188, G.189, K.190, T.191, D.243, E.244, A.288, N.290, I.322, H.326, G.350, A.351 5 PLIP interactions: 5 interactions with chain i Hydrogen bonds: i:K.190, i:K.190, i:T.191, i:D.243 Salt bridges: i:K.190

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

26S proteasome non-ATPase regulatory subunit 1: A
26S proteasome non-ATPase regulatory subunit 3: B
26S proteasome non-ATPase regulatory subunit 12: C
26S proteasome non-ATPase regulatory subunit 11: D
26S proteasome non-ATPase regulatory subunit 6: E
26S proteasome non-ATPase regulatory subunit 7: F
26S proteasome non-ATPase regulatory subunit 13: G
26S proteasome non-ATPase regulatory subunit 4: H
26S proteasome non-ATPase regulatory subunit 14: I
26S proteasome non-ATPase regulatory subunit 8: J
Sem1: K
Proteasome subunit alpha type-6: LZ
Proteasome subunit alpha type-2: M0
Proteasome subunit alpha type-4: N1
Proteasome subunit alpha type-7: O2
Proteasome subunit alpha type-5: P3
Proteasome subunit alpha type-1: Q4
Proteasome subunit alpha type-3: R5
Proteasome subunit beta type-6: S6
Proteasome subunit beta type-7: T7
Proteasome subunit beta type-3: U8
Proteasome subunit beta type-2: V9
Proteasome subunit beta type-5: Wa
Proteasome subunit beta type-1: Xb
Proteasome subunit beta type-4: Yc
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
U

B
V

C
W

D
X

E
Y

F
Z

G
a

H
b

I
c

J
d

K
e

L
G

Z
g

M
H

0
h

N
I

1
i

O
J

2
j

P
K

3
k

Q
L

4
l

R
M

5
m

S
N

6
n

T
O

7
o

U
P

8
p

V
Q

9
q

W
R

a
r

X
S

b
s

Y
T

c
t

d
A

e
B

f
C

g
D

h
E

i
F

j
f

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

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 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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