SMTL ID : 6ef3.1

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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

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

ATP.1: 16 residues within 4Å: Chain O: V.211, G.212, P.252, G.253, T.254, G.255, K.256, T.257, L.258, E.310, N.356, H.392, R.420 Chain P: L.310, R.340, R.343 20 PLIP interactions: 16 interactions with chain O, 4 interactions with chain P Hydrogen bonds: O:G.212, O:T.254, O:T.254, O:G.255, O:K.256, O:T.257, O:T.257, O:T.257, O:L.258, O:E.310, O:E.310, O:N.356, O:R.420 Salt bridges: O:K.256, O:K.256, O:K.256, P:R.340, P:R.340, P:R.340, P:R.343 ATP.2: 19 residues within 4Å: Chain P: I.184, G.186, G.226, T.227, G.228, K.229, T.230, L.231, D.282, E.283, N.329, I.361, H.365, G.389, A.390, Q.393 Chain Q: L.273, R.306, R.309 18 PLIP interactions: 14 interactions with chain P, 4 interactions with chain Q Hydrogen bonds: P:G.186, P:G.226, P:T.227, P:G.228, P:K.229, P:T.230, P:T.230, P:T.230, P:L.231, P:D.282, P:E.283, P:N.329 Salt bridges: P:K.229, P:K.229, Q:R.306, Q:R.306, Q:R.309, Q:R.309 ATP.3: 15 residues within 4Å: Chain Q: M.149, V.150, G.151, G.192, T.193, G.194, K.195, T.196, L.197, N.295, I.327, I.330, H.331, G.355, A.356 15 PLIP interactions: 15 interactions with chain Q Hydrogen bonds: Q:G.151, Q:G.151, Q:G.192, Q:T.193, Q:G.194, Q:K.195, Q:T.196, Q:T.196, Q:T.196, Q:T.196, Q:L.197, Q:N.295 Salt bridges: Q:K.195, Q:K.195, Q:K.195 ATP.6: 21 residues within 4Å: Chain O: R.367, R.370 Chain T: V.183, G.184, L.186, P.223, P.224, G.225, T.226, G.227, K.228, T.229, L.230, D.281, E.282, N.328, I.360, H.364, G.388, A.389, K.392 14 PLIP interactions: 10 interactions with chain T, 4 interactions with chain O Hydrogen bonds: T:G.184, T:G.184, T:G.225, T:G.227, T:K.228, T:T.229, T:L.230, T:E.282, T:E.282, T:N.328 Salt bridges: O:R.367, O:R.367, O:R.367, O:R.370

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

ADP.4: 12 residues within 4Å: Chain R: V.174, G.175, P.215, G.216, T.217, G.218, K.219, T.220, D.272, I.352, G.380, A.381 8 PLIP interactions: 8 interactions with chain R Hydrogen bonds: R:G.175, R:G.216, R:T.217, R:G.218, R:K.219, R:T.220, R:D.272 Salt bridges: R:K.219 ADP.5: 9 residues within 4Å: Chain S: G.184, T.226, G.227, K.228, T.229, H.364, G.388, A.389, R.392 9 PLIP interactions: 9 interactions with chain S Hydrogen bonds: S:G.184, S:G.225, S:T.226, S:G.227, S:K.228, S:T.229, S:T.229, S:T.229 Salt bridges: S:K.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de la Pena, A.H. et al., Substrate-engaged 26Sproteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation. Science (2018)

Release Date

2018-10-17

Peptides

Proteasome subunit beta type-1: A
Proteasome subunit beta type-2: B
Proteasome subunit beta type-3: C
Proteasome subunit beta type-4: D
Proteasome subunit beta type-5: E
Proteasome subunit beta type-6: F
Proteasome subunit beta type-7: G
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 7 homolog: O
26S proteasome regulatory subunit 4 homolog: P
26S proteasome regulatory subunit 8 homolog: Q
26S proteasome regulatory subunit 6B homolog: R
26S proteasome subunit RPT4: S
26S proteasome regulatory subunit 6A: T
Proteasome subunit beta type-7: U
Ubiquitin carboxyl-terminal hydrolase RPN11: V
Model substrate polypeptide: W
Ubiquitin-60S ribosomal protein L40: X

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
7

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
H

P
I

Q
J

R
K

S
L

T
M

U
n

V
r

W
s

X
u

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 7 homolog

26S proteasome regulatory subunit 4 homolog

26S proteasome regulatory subunit 8 homolog

26S proteasome regulatory subunit 6B homolog

26S proteasome subunit RPT4

26S proteasome regulatory subunit 6A

Proteasome subunit beta type-7

Ubiquitin carboxyl-terminal hydrolase RPN11

Model substrate polypeptide

Ubiquitin-60S ribosomal protein L40

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