SMTL ID : 6ef0.1

Yeast 26S proteasome bound to ubiquitinated substrate (1D* 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

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

ADP.1: 15 residues within 4Å: Chain H: D.10, V.11, G.12, G.13, P.52, G.53, G.55, K.56, T.57, L.58, H.192, G.216, A.217, R.220 Chain I: R.175 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:G.12, H:G.53, H:T.54, H:G.55, H:T.57, H:T.57, H:T.57, H:A.217, H:R.220 Salt bridges: I:R.175 ADP.5: 14 residues within 4Å: Chain L: G.19, I.20, G.21, P.61, G.62, T.63, G.64, K.65, T.66, L.67, I.197, G.225, A.226, R.229 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.21, L:G.62, L:T.63, L:G.64, L:K.65, L:T.66, L:T.66, L:T.66, L:L.67 Salt bridges: L:K.65 ADP.6: 14 residues within 4Å: Chain M: D.7, V.8, P.49, G.50, T.51, G.52, K.53, T.54, L.55, I.185, H.189, G.213, A.214, K.217 7 PLIP interactions: 7 interactions with chain M Hydrogen bonds: M:V.8, M:G.50, M:T.54, M:T.54, M:T.54, M:L.55 Salt bridges: M:K.53

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

ATP.2: 17 residues within 4Å: Chain I: G.20, A.59, G.61, T.62, G.63, K.64, T.65, L.66, D.117, I.196, G.224, A.225, Q.228 Chain J: L.144, N.148, R.177, R.180 19 PLIP interactions: 5 interactions with chain J, 14 interactions with chain I Hydrogen bonds: J:L.144, I:G.20, I:G.61, I:T.62, I:G.63, I:K.64, I:T.65, I:T.65, I:T.65, I:T.65, I:D.117, I:Q.228 Salt bridges: J:R.177, J:R.177, J:R.177, J:R.180, I:K.64, I:K.64, I:K.64 ATP.3: 20 residues within 4Å: Chain J: M.20, V.21, G.22, G.63, T.64, G.65, K.66, T.67, L.68, D.119, E.120, I.198, H.202, G.226, A.227, K.230 Chain K: L.144, D.148, R.174, R.177 18 PLIP interactions: 14 interactions with chain J, 4 interactions with chain K Hydrogen bonds: J:G.22, J:G.63, J:T.64, J:G.65, J:K.66, J:T.67, J:T.67, J:D.119, J:E.120, J:E.120, J:K.230 Salt bridges: J:K.66, J:K.66, J:K.66, K:R.174, K:R.174, K:R.177, K:R.177 ATP.4: 16 residues within 4Å: Chain K: V.18, G.19, G.60, T.61, G.62, K.63, T.64, M.65, D.116, T.162, N.163, G.224, A.225 Chain L: L.146, R.176, R.179 17 PLIP interactions: 12 interactions with chain K, 5 interactions with chain L Hydrogen bonds: K:G.19, K:G.19, K:G.60, K:G.62, K:G.62, K:K.63, K:T.64, K:T.64, K:M.65, K:D.116, K:T.162, K:N.163, L:R.176 Salt bridges: L:R.176, L:R.176, L:R.179, L:R.179

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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