SMTL ID : 9cgc.1

Yeast 26S proteasome non-substrate-engaged (S1 state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain 5: R.309 Chain O: K.229, T.230 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.230 MG.3: 4 residues within 4Å: Chain P: T.220 Chain Q: D.313, R.339 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.220 MG.5: 3 residues within 4Å: Chain Q: T.229, E.282 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.229 MG.10: 3 residues within 4Å: Chain 6: T.257 Chain O: R.343 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:T.257 MG.12: 2 residues within 4Å: Chain 7: T.229 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain 7 Metal complexes: 7:T.229

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

ATP.2: 18 residues within 4Å: Chain P: G.175, L.177, G.216, T.217, G.218, K.219, T.220, M.221, E.273, N.319, I.352, I.356, G.380, A.381, A.384 Chain Q: R.339, R.342 Ligands: MG.3 17 PLIP interactions: 13 interactions with chain P, 4 interactions with chain Q Hydrogen bonds: P:G.175, P:G.175, P:G.216, P:T.217, P:G.218, P:K.219, P:T.220, P:T.220, P:M.221, P:N.319, P:N.319 Salt bridges: P:K.219, P:K.219, Q:R.339, Q:R.339, Q:R.339, Q:R.342 ATP.4: 17 residues within 4Å: Chain 7: R.339, R.342 Chain Q: G.182, G.184, P.224, G.225, T.226, G.227, K.228, T.229, L.230, E.282, N.328, I.360, H.364, A.389 Ligands: MG.5 18 PLIP interactions: 15 interactions with chain Q, 3 interactions with chain 7 Hydrogen bonds: Q:G.184, Q:G.184, Q:G.225, Q:G.225, Q:T.226, Q:G.227, Q:K.228, Q:T.229, Q:L.230, Q:E.282, Q:N.328, Q:N.328, Q:A.389 Salt bridges: Q:K.228, Q:K.228, 7:R.339, 7:R.339, 7:R.342 ATP.7: 19 residues within 4Å: Chain 5: R.306, R.309 Chain O: D.183, I.184, G.185, P.225, G.226, T.227, G.228, K.229, T.230, L.231, E.283, N.329, I.361, H.365, G.389, A.390 Ligands: MG.1 14 PLIP interactions: 11 interactions with chain O, 3 interactions with chain 5 Hydrogen bonds: O:G.185, O:G.185, O:G.226, O:T.227, O:G.228, O:K.229, O:T.230, O:L.231, O:N.329 Salt bridges: O:K.229, O:K.229, 5:R.306, 5:R.306, 5:R.309 ATP.9: 22 residues within 4Å: Chain 6: D.210, V.211, G.212, C.214, P.252, G.253, T.254, G.255, K.256, T.257, L.258, E.310, N.356, I.388, H.392, G.416, A.417, R.420 Chain O: D.314, R.340, R.343 Ligands: MG.10 14 PLIP interactions: 10 interactions with chain 6, 4 interactions with chain O Hydrogen bonds: 6:G.212, 6:G.212, 6:G.253, 6:T.254, 6:G.255, 6:K.256, 6:T.257, 6:L.258, O:D.314 Salt bridges: 6:K.256, 6:K.256, O:R.340, O:R.340, O:R.343 ATP.11: 23 residues within 4Å: Chain 6: I.337, D.341, R.367, R.370 Chain 7: D.182, V.183, G.184, P.223, P.224, G.225, T.226, G.227, K.228, T.229, L.230, D.281, E.282, I.360, H.364, G.388, A.389, K.392 Ligands: MG.12 18 PLIP interactions: 15 interactions with chain 7, 3 interactions with chain 6 Hydrogen bonds: 7:G.184, 7:G.184, 7:G.225, 7:G.227, 7:G.227, 7:K.228, 7:T.229, 7:T.229, 7:L.230, 7:E.282, 7:E.282, 7:A.389, 7:K.392 Salt bridges: 7:K.228, 7:K.228, 6:R.367, 6:R.367, 6:R.370

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain V: E.48, V.80, H.109, H.111, S.119, D.122 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.48, V:H.109, V:H.111, V:D.122, V:D.122

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

ADP.8: 14 residues within 4Å: Chain 5: M.149, G.151, P.191, 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 5 Hydrogen bonds: 5:G.151, 5:G.151, 5:G.192, 5:T.193, 5:G.194, 5:K.195, 5:T.196 Salt bridges: 5:K.195, 5:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Alfonzo, E.M. et al., Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome. To Be Published

Release Date

2025-07-09

Peptides

Proteasome subunit beta type-1: AZ
Proteasome subunit beta type-2: B4
Proteasome subunit beta type-3: C3
Proteasome subunit beta type-4: D2
Proteasome subunit beta type-5: E1
Proteasome subunit beta type-6: F0
Proteasome subunit beta type-7: GY
Proteasome subunit alpha type-1: H
Proteasome subunit alpha type-2: I
Proteasome subunit alpha type-3: J
Proteasome subunit alpha type-4: K
Proteasome subunit alpha type-5: L
Proteasome subunit alpha type-6: M
Probable proteasome subunit alpha type-7: N
26S proteasome regulatory subunit 4 homolog: O
26S proteasome regulatory subunit 6B homolog: P
26S proteasome subunit RPT4: Q
26S proteasome regulatory subunit RPN9: R
26S proteasome regulatory subunit RPN5: S
26S proteasome regulatory subunit RPN7: T
26S proteasome regulatory subunit RPN3: U
Ubiquitin carboxyl-terminal hydrolase RPN11: V
26S proteasome regulatory subunit RPN10: W
26S proteasome complex subunit SEM1: X
26S proteasome regulatory subunit 8 homolog: 5
26S proteasome regulatory subunit 7 homolog: 6
26S proteasome regulatory subunit 6A: 7
26S proteasome regulatory subunit RPN6: 8
26S proteasome regulatory subunit RPN8: 9
26S proteasome regulatory subunit RPN2: a
26S proteasome regulatory subunit RPN12: b
26S proteasome regulatory subunit RPN1: c

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

Z
b

B
2

4
i

C
3

3
h

D
4

2
g

E
5

1
f

F
6

0
e

G
7

Y
a

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
I

P
K

Q
L

R
O

S
P

T
R

U
S

V
V

W
W

X
Y

5
J

6
H

7
M

8
Q

9
U

a
N

b
T

c
o

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

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

26S proteasome regulatory subunit 4 homolog

26S proteasome regulatory subunit 6B homolog

26S proteasome subunit RPT4

26S proteasome regulatory subunit RPN9

26S proteasome regulatory subunit RPN5

26S proteasome regulatory subunit RPN7

26S proteasome regulatory subunit RPN3

Ubiquitin carboxyl-terminal hydrolase RPN11

26S proteasome regulatory subunit RPN10

26S proteasome complex subunit SEM1

26S proteasome regulatory subunit 8 homolog

26S proteasome regulatory subunit 7 homolog

26S proteasome regulatory subunit 6A

26S proteasome regulatory subunit RPN6

26S proteasome regulatory subunit RPN8

26S proteasome regulatory subunit RPN2

26S proteasome regulatory subunit RPN12

26S proteasome regulatory subunit RPN1

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