SMTL ID : 7qo5.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Ligands: MG.2 Chain f: G.212, P.252, G.253, T.254, G.255, K.256, T.257, L.258, R.261, N.356, I.388, H.392, G.416, A.417, R.420 Chain g: D.314, G.315, A.337, R.340, R.343 19 PLIP interactions: 15 interactions with chain f, 4 interactions with chain g Hydrogen bonds: f:G.253, f:T.254, f:T.254, f:T.254, f:G.255, f:K.256, f:T.257, f:T.257, f:L.258, f:R.261, f:R.261, f:N.356, g:R.340, g:R.340 Salt bridges: f:K.256, f:K.256, f:R.261, g:R.343, g:R.343 ATP.3: 20 residues within 4Å: Ligands: MG.4 Chain g: D.183, I.184, G.185, 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: E.274, N.277, R.306, R.309 12 PLIP interactions: 3 interactions with chain k, 9 interactions with chain g Hydrogen bonds: k:N.277, g:G.185, g:G.226, g:T.227, g:G.228, g:K.229, g:T.230, g:T.230, g:L.231 Salt bridges: k:R.306, k:R.309, g:K.229 ATP.5: 15 residues within 4Å: Ligands: MG.6 Chain h: L.177, P.215, G.216, T.217, G.218, K.219, T.220, M.221, N.319, I.356, G.380 Chain i: D.313, R.339, R.342 17 PLIP interactions: 10 interactions with chain h, 7 interactions with chain i Hydrogen bonds: h:G.216, h:T.217, h:G.218, h:K.219, h:T.220, h:M.221, h:N.319, h:N.319, i:K.213, i:R.339, i:R.342 Salt bridges: h:K.219, h:K.224, i:R.339, i:R.339, i:R.339, i:R.342 ATP.7: 18 residues within 4Å: Ligands: MG.8 Chain i: I.183, P.224, G.225, T.226, G.227, K.228, T.229, L.230, K.233, E.282, N.328, H.364, G.388, A.389 Chain j: D.313, R.339, R.342 23 PLIP interactions: 10 interactions with chain j, 13 interactions with chain i Hydrogen bonds: j:D.313, j:D.313, j:G.314, j:R.339, i:G.225, i:T.226, i:T.226, i:G.227, i:K.228, i:T.229, i:L.230, i:K.233, i:E.282, i:N.328, i:N.328 Salt bridges: j:R.339, j:R.339, j:R.339, j:R.342, j:R.342, j:R.342, i:K.228, i:K.228 ATP.9: 17 residues within 4Å: Ligands: MG.10 Chain f: D.341, R.367 Chain j: G.184, P.224, G.225, T.226, G.227, K.228, T.229, L.230, N.328, I.360, H.364, G.388, A.389, K.392 15 PLIP interactions: 4 interactions with chain f, 11 interactions with chain j Hydrogen bonds: f:R.370, j:G.184, j:G.225, j:T.226, j:G.227, j:K.228, j:T.229, j:T.229, j:L.230, j:N.328 Salt bridges: f:R.367, f:R.367, f:R.367, j:K.228, j:K.228

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Ligands: ATP.1 Chain f: E.310 1 PLIP interactions: 1 interactions with chain f Metal complexes: f:E.310 MG.4: 4 residues within 4Å: Ligands: ATP.3 Chain g: T.230 Chain k: E.274, N.277 1 PLIP interactions: 1 interactions with chain g Metal complexes: g:T.230 MG.6: 3 residues within 4Å: Ligands: ATP.5 Chain h: T.220 Chain i: R.342 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 Chain j: R.342 1 PLIP interactions: 1 interactions with chain i Metal complexes: i:T.229 MG.10: 4 residues within 4Å: Ligands: ATP.9 Chain f: D.341 Chain j: T.229, D.281 2 PLIP interactions: 1 interactions with chain f, 1 interactions with chain j Metal complexes: f:D.341, j:T.229 MG.12: 3 residues within 4Å: Ligands: ADP.11 Chain k: K.195, D.248 1 PLIP interactions: 1 interactions with chain k Metal complexes: k:D.248

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

ADP.11: 17 residues within 4Å: Ligands: MG.12 Chain k: M.149, V.150, G.151, L.153, P.190, G.192, T.193, G.194, K.195, T.196, L.197, I.327, H.331, G.355, A.356, K.359 9 PLIP interactions: 9 interactions with chain k Hydrogen bonds: k:V.150, k:G.192, k:T.193, k:G.194, k:K.195, k:T.196, k:T.196, k:T.196 Salt bridges: k:K.195

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

Proteasome subunit alpha type-1: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-3: CQ
Proteasome subunit alpha type-4: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-6: FT
Probable proteasome subunit alpha type-7: GU
Proteasome subunit beta type-1: HV
Proteasome subunit beta type-2: IW
Proteasome subunit beta type-3: JX
Proteasome subunit beta type-4: KY
Proteasome subunit beta type-5: LZ
Proteasome subunit beta type-6: M0
Proteasome subunit beta type-7: N1
26S proteasome regulatory subunit RPN10: 2
Ubiquitin carboxyl-terminal hydrolase RPN11: 3
26S proteasome regulatory subunit RPN12: 4
26S proteasome regulatory subunit RPN13: 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 6: 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

Proteasome subunit alpha type-1

Proteasome subunit alpha type-2

Proteasome subunit alpha type-3

Proteasome subunit alpha type-4

Proteasome subunit alpha type-5

Proteasome subunit alpha type-6

Probable proteasome subunit alpha type-7

Proteasome subunit beta type-1

Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-5

Proteasome subunit beta type-6

Proteasome subunit beta type-7

26S proteasome regulatory subunit RPN10

Ubiquitin carboxyl-terminal hydrolase RPN11

26S proteasome regulatory subunit RPN12

26S proteasome regulatory subunit RPN13

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 6

Polyubiquitin-B

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