SMTL ID : 6ef2.1

Yeast 26S proteasome bound to ubiquitinated substrate (5T 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-mer

Ligands

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

ATP.1: 20 residues within 4Å: Chain H: D.17, G.19, P.58, P.59, G.60, T.61, G.62, K.63, T.64, E.117, N.163, I.195, I.198, H.199, G.223, A.224, R.227 Chain I: D.137, R.163, R.166 14 PLIP interactions: 10 interactions with chain H, 4 interactions with chain I Hydrogen bonds: H:G.19, H:G.60, H:T.61, H:G.62, H:K.63, H:T.64, H:R.227 Salt bridges: H:K.63, H:K.63, H:K.63, I:R.163, I:R.163, I:R.163, I:R.166 ATP.2: 19 residues within 4Å: Chain I: D.6, I.7, P.48, G.49, T.50, G.51, K.52, T.53, L.54, E.106, N.152, I.184, H.188, G.212, A.213, Q.216 Chain J: L.130, N.134, R.163 17 PLIP interactions: 5 interactions with chain J, 12 interactions with chain I Hydrogen bonds: J:N.134, J:N.134, J:R.166, I:I.7, I:G.49, I:T.50, I:G.51, I:K.52, I:T.53, I:L.54, I:N.152, I:Q.216 Salt bridges: J:R.163, J:R.163, I:K.52, I:K.52, I:K.52 ATP.3: 16 residues within 4Å: Chain J: M.6, G.8, G.49, T.50, G.51, K.52, T.53, L.54, D.105, E.106, H.188, G.212, A.213 Chain K: D.135, R.161, R.164 18 PLIP interactions: 4 interactions with chain K, 14 interactions with chain J Hydrogen bonds: K:D.135, K:R.164, J:G.8, J:G.49, J:T.50, J:G.51, J:K.52, J:T.53, J:T.53, J:L.54, J:D.105, J:E.106, J:E.106 Salt bridges: K:R.161, K:R.161, J:K.52, J:K.52, J:K.52 ATP.6: 18 residues within 4Å: Chain H: R.174 Chain M: D.18, V.19, G.20, L.22, P.60, G.61, T.62, G.63, K.64, T.65, L.66, N.164, I.196, H.200, G.224, A.225, K.228 16 PLIP interactions: 2 interactions with chain H, 14 interactions with chain M Salt bridges: H:R.174, H:R.174, M:K.64, M:K.64, M:K.64 Hydrogen bonds: M:G.20, M:G.20, M:G.61, M:T.62, M:G.63, M:K.64, M:T.65, M:T.65, M:T.65, M:L.66, M:N.164

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

ADP.4: 12 residues within 4Å: Chain K: G.6, P.46, G.47, T.48, G.49, K.50, T.51, M.52, D.103, N.150, G.211, A.212 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:G.6, K:G.47, K:T.48, K:G.49, K:K.50, K:T.51, K:T.51, K:D.103, K:N.150 Salt bridges: K:K.50, K:K.50 ADP.5: 14 residues within 4Å: Chain L: I.18, G.19, G.20, P.59, G.60, T.61, G.62, K.63, T.64, L.65, I.195, H.199, G.223, A.224 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:G.19, L:G.19, L:G.60, L:G.62, L:K.63, L:T.64 Salt bridges: L:K.63, L:K.63

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 alpha type-1: A
Proteasome subunit alpha type-2: B
Proteasome subunit alpha type-3: C
Proteasome subunit alpha type-4: D
Proteasome subunit alpha type-5: E
Proteasome subunit alpha type-6: F
Probable proteasome subunit alpha type-7: G
26S proteasome regulatory subunit 7 homolog: H
26S proteasome regulatory subunit 4 homolog: I
26S proteasome regulatory subunit 8 homolog: J
26S proteasome regulatory subunit 6B homolog: K
26S proteasome subunit RPT4: L
26S proteasome regulatory subunit 6A: M
model substrate polypeptide: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
s

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

model substrate polypeptide

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