SMTL ID : 7qo6.1

26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.1: 20 residues within 4Å: Ligands: MG.2 Chain f: D.210, V.211, G.212, P.252, G.253, T.254, G.255, K.256, T.257, L.258, R.261, N.356, I.388, H.392, R.420 Chain g: D.314, A.337, R.340, R.343 18 PLIP interactions: 13 interactions with chain f, 5 interactions with chain g Hydrogen bonds: f:G.212, f:G.253, f:T.254, f:G.255, f:K.256, f:T.257, f:T.257, f:L.258 Salt bridges: f:K.256, f:K.256, f:R.261, g:R.340, g:R.340, g:R.340, g:R.343, g:R.343 pi-Cation interactions: f:R.420, f:R.420 ATP.3: 20 residues within 4Å: Ligands: MG.4 Chain g: D.183, I.184, G.185, G.186, L.187, P.225, G.226, T.227, G.228, K.229, T.230, L.231, I.361, H.365, G.389, A.390, Q.393 Chain k: R.306, R.309 13 PLIP interactions: 9 interactions with chain g, 4 interactions with chain k Hydrogen bonds: g:G.186, g:G.226, g:G.228, g:K.229, g:T.230, g:L.231, g:E.283, g:Q.393 Salt bridges: g:K.229, k:R.306, k:R.309, k:R.309, k:R.309 ATP.5: 17 residues within 4Å: Ligands: MG.6 Chain h: D.173, V.174, L.177, P.215, G.216, G.218, K.219, T.220, M.221, E.273, N.319, G.380, A.381 Chain i: L.309, R.339, R.342 11 PLIP interactions: 7 interactions with chain h, 4 interactions with chain i Hydrogen bonds: h:G.218, h:K.219, h:T.220, h:M.221, h:E.273, h:E.273, h:E.273, i:R.339 Salt bridges: i:R.339, i:R.339, i:R.342 ATP.7: 16 residues within 4Å: Ligands: MG.8 Chain i: I.183, G.225, T.226, G.227, K.228, T.229, L.230, E.282, N.328, H.364, G.388, A.389 Chain j: D.313, R.339, R.342 18 PLIP interactions: 13 interactions with chain i, 5 interactions with chain j Hydrogen bonds: i:G.225, i:G.225, i:T.226, i:G.227, i:K.228, i:T.229, i:T.229, i:T.229, i:L.230, i:E.282, i:N.328, j:D.313 Salt bridges: i:K.228, i:K.233, j:R.339, j:R.339, j:R.339, j:R.342 ATP.9: 18 residues within 4Å: Ligands: MG.10 Chain f: R.367, R.370 Chain j: D.182, V.183, G.184, L.186, P.224, G.225, T.226, G.227, K.228, T.229, L.230, R.233, N.328, I.360, H.364 17 PLIP interactions: 13 interactions with chain j, 4 interactions with chain f Hydrogen bonds: j:G.184, j:G.184, j:G.225, j:T.226, j:T.226, j:G.227, j:K.228, j:T.229, j:L.230, j:R.233, f:R.370 Salt bridges: j:K.228, j:K.228, j:K.228, f:R.367, f:R.367, f:R.367

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Ligands: ATP.1 Chain f: T.257 1 PLIP interactions: 1 interactions with chain f Metal complexes: f:T.257 MG.4: 5 residues within 4Å: Ligands: ATP.3 Chain g: T.230, E.283 Chain k: E.274, R.309 1 PLIP interactions: 1 interactions with chain g Metal complexes: g:T.230 MG.6: 2 residues within 4Å: Ligands: ATP.5 Chain h: T.220 1 PLIP interactions: 1 interactions with chain h Metal complexes: h:T.220 MG.8: 3 residues within 4Å: Ligands: ATP.7 Chain i: T.229, E.282 1 PLIP interactions: 1 interactions with chain i Metal complexes: i:T.229 MG.10: 6 residues within 4Å: Ligands: ATP.9 Chain f: D.341 Chain j: K.228, T.229, D.281, E.282 1 PLIP interactions: 1 interactions with chain j Metal complexes: j:T.229 MG.12: 3 residues within 4Å: Ligands: ADP.11 Chain k: T.196, D.248 1 PLIP interactions: 1 interactions with chain k Metal complexes: k:T.196

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

ADP.11: 15 residues within 4Å: Ligands: MG.12 Chain k: M.149, V.150, G.151, P.191, G.192, T.193, G.194, K.195, T.196, L.197, R.200, I.327, G.355, K.359 12 PLIP interactions: 12 interactions with chain k Hydrogen bonds: k:G.151, k:G.192, k:T.193, k:G.194, k:K.195, k:T.196, k:T.196, k:L.197, k:K.359, k:K.359 Salt bridges: k:K.195, k:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hung, K.Y.S. et al., Allosteric control of Ubp6 and the proteasome via a bidirectional switch. Nat Commun (2022)

Release Date

2022-03-16

Peptides

BJ4_G0020160.mRNA.1.CDS.1: AO
HLJ1_G0039880.mRNA.1.CDS.1: BP
BJ4_G0021480.mRNA.1.CDS.1: CQ
HLJ1_G0048980.mRNA.1.CDS.1: DR
EM14S01-3B_G0035190.mRNA.1.CDS.1: ES
BJ4_G0043800.mRNA.1.CDS.1: FT
Probable proteasome subunit alpha type-7: GU
Proteasome subunit beta type-1: HV
Proteasome endopeptidase complex: IW
Proteasome endopeptidase complex: JX
Proteasome subunit beta: KY
Proteasome subunit beta type-5: LZ
HLJ1_G0013750.mRNA.1.CDS.1: M0
Proteasome subunit beta type-7: N1
26S proteasome regulatory subunit RPN10: 2
26S proteasome regulatory subunit RPN11: 3
EM14S01-3B_G0050020.mRNA.1.CDS.1: 4
HLJ1_G0030700.mRNA.1.CDS.1: 5
26S proteasome complex subunit SEM1: 6
26S proteasome regulatory subunit RPN1: 7
26S proteasome regulatory subunit RPN2: 8
26S proteasome regulatory subunit RPN3: 9
26S proteasome regulatory subunit RPN5: a
26S proteasome regulatory subunit RPN6: b
26S proteasome regulatory subunit RPN7: c
26S proteasome regulatory subunit RPN8: d
26S proteasome regulatory subunit RPN9: e
26S proteasome regulatory subunit 7 homolog: f
26S proteasome regulatory subunit 4 homolog: g
26S proteasome regulatory subunit 6B homolog: h
26S proteasome subunit RPT4: i
26S proteasome regulatory subunit 6A: j
26S proteasome regulatory subunit 8 homolog: k
Ubiquitin carboxyl-terminal hydrolase: l
Polyubiquitin-B: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

O
A

B
b

P
B

C
c

Q
C

D
d

R
D

E
e

S
E

F
f

T
F

G
g

U
G

H
h

V
1

I
i

W
2

J
j

X
3

K
k

Y
4

L
l

Z
5

M
m

0
6

N
n

1
7

2
W

3
V

4
T

5
X

6
Y

7
Z

8
N

9
S

a
P

b
Q

c
R

d
U

e
O

f
H

g
I

h
K

i
L

j
M

k
J

l
8

m
9

BJ4_G0020160.mRNA.1.CDS.1

HLJ1_G0039880.mRNA.1.CDS.1

BJ4_G0021480.mRNA.1.CDS.1

HLJ1_G0048980.mRNA.1.CDS.1

EM14S01-3B_G0035190.mRNA.1.CDS.1

BJ4_G0043800.mRNA.1.CDS.1

Probable proteasome subunit alpha type-7

Proteasome subunit beta type-1

Proteasome endopeptidase complex

Proteasome endopeptidase complex

Proteasome subunit beta

Proteasome subunit beta type-5

HLJ1_G0013750.mRNA.1.CDS.1

Proteasome subunit beta type-7

26S proteasome regulatory subunit RPN10

26S proteasome regulatory subunit RPN11

EM14S01-3B_G0050020.mRNA.1.CDS.1

HLJ1_G0030700.mRNA.1.CDS.1

26S proteasome complex subunit SEM1

26S proteasome regulatory subunit RPN1

26S proteasome regulatory subunit RPN2

26S proteasome regulatory subunit RPN3

26S proteasome regulatory subunit RPN5

26S proteasome regulatory subunit RPN6

26S proteasome regulatory subunit RPN7

26S proteasome regulatory subunit RPN8

26S proteasome regulatory subunit RPN9

26S proteasome regulatory subunit 7 homolog

26S proteasome regulatory subunit 4 homolog

26S proteasome regulatory subunit 6B homolog

26S proteasome subunit RPT4

26S proteasome regulatory subunit 6A

26S proteasome regulatory subunit 8 homolog

Ubiquitin carboxyl-terminal hydrolase

Polyubiquitin-B

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