SMTL ID : 5vfp.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 V: H.92, S.100, D.103 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:H.92, V:S.100

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

AGS.2: 18 residues within 4Å: Chain d: D.142, G.144, P.184, G.185, T.186, G.187, K.188, T.189, L.190, E.242, N.288, I.320, H.324, G.348, A.349 Chain e: D.266, R.292, R.295 17 PLIP interactions: 11 interactions with chain d, 6 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:N.288, d:G.348, e:D.266, e:R.292, e:R.292, e:R.295 Salt bridges: d:K.188, d:K.188, e:R.292, e:R.292 AGS.3: 19 residues within 4Å: Chain g: D.128, I.129, G.130, M.132, 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: 2 interactions with chain h, 12 interactions with chain g Hydrogen bonds: h:D.251, g:G.130, g:G.130, g:G.173, g:K.174, g:K.174, g:T.175, g:T.175, g:M.176, g:K.179, g:N.338 Salt bridges: h:R.277, g:K.174, g:K.179 AGS.4: 19 residues within 4Å: Chain h: G.122, L.124, P.162, G.163, T.164, G.165, K.166, T.167, L.168, N.266, I.298, H.302, G.326, A.327, R.330 Chain i: D.275, A.298, R.301, R.304 15 PLIP interactions: 10 interactions with chain h, 5 interactions with chain i Hydrogen bonds: h:G.122, h:G.163, h:K.166, h:K.166, h:T.167, h:T.167, h:N.266, h:R.330, i:R.304, i:R.304 Salt bridges: h:K.166, h:K.166, i:R.301, i:R.304, i:R.304 AGS.5: 19 residues within 4Å: Chain d: R.299, R.302 Chain i: D.144, I.145, G.146, L.148, P.185, P.186, G.187, T.188, G.189, K.190, T.191, L.192, N.290, I.322, I.325, G.350, A.351 15 PLIP interactions: 10 interactions with chain i, 5 interactions with chain d Hydrogen bonds: i:G.146, i:G.146, i:P.186, i:G.189, i:K.190, i:K.190, i:T.191, i:T.191, i:T.191, i:N.290, d:R.299, d:R.302 Salt bridges: d:R.299, d:R.299, d:R.302

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: AY
Proteasome subunit alpha type-2: BZ
Proteasome subunit alpha type-4: C0
Proteasome subunit alpha type-7: D1
Proteasome subunit alpha type-5: E2
Proteasome subunit alpha type-1: F3
Proteasome subunit alpha type-3: G4
Proteasome subunit beta type-6: H5
Proteasome subunit beta type-7: I6
Proteasome subunit beta type-3: J7
Proteasome subunit beta type-2: K8
Proteasome subunit beta type-5: L9
Proteasome subunit beta type-1: Ma
Proteasome subunit beta type-4: Nb
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 6: R
26S proteasome non-ATPase regulatory subunit 7: S
26S proteasome non-ATPase regulatory subunit 13: T
26S proteasome non-ATPase regulatory subunit 4: U
26S proteasome non-ATPase regulatory subunit 14: V
26S proteasome non-ATPase regulatory subunit 8: W
sem1: X
26S proteasome non-ATPase regulatory subunit 11: c
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

Y
g

B
H

Z
h

C
I

0
i

D
J

1
j

E
K

2
k

F
L

3
l

G
M

4
m

H
N

5
n

I
O

6
o

J
P

7
p

K
Q

8
q

L
R

9
r

M
S

a
s

N
T

b
t

O
U

P
V

Q
W

R
Y

S
Z

T
a

U
b

V
c

W
d

X
e

c
X

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 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 non-ATPase regulatory subunit 11

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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