SMTL ID : 6ef1.1

Yeast 26S proteasome bound to ubiquitinated substrate (5D 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: 17 residues within 4Å: Chain H: V.18, G.19, G.20, P.59, G.60, T.61, G.62, K.63, T.64, E.117, I.195, G.223, A.224, R.227 Chain I: L.144, D.148, R.174 16 PLIP interactions: 13 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:G.19, H:G.20, H:G.60, H:T.61, H:G.62, H:T.64, H:T.64, H:L.65, H:E.117, H:G.223, H:A.224 Salt bridges: H:K.63, H:K.63, I:R.174, I:R.174, I:R.174 ATP.2: 14 residues within 4Å: Chain I: I.18, G.60, T.61, G.62, K.63, T.64, L.65, E.117, I.195, A.224, Q.227 Chain J: L.141, N.145, R.177 15 PLIP interactions: 2 interactions with chain J, 13 interactions with chain I Salt bridges: J:R.177, J:R.177, I:K.63, I:K.63, I:K.63 Hydrogen bonds: I:G.60, I:T.61, I:G.62, I:K.63, I:T.64, I:T.64, I:T.64, I:L.65, I:E.117, I:E.117 ATP.3: 16 residues within 4Å: Chain J: M.17, V.18, G.19, L.21, P.59, G.60, T.61, G.62, K.63, T.64, L.65, I.195, G.223, A.224, K.227 Chain K: R.178 11 PLIP interactions: 9 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:V.18, J:G.60, J:T.61, J:G.62, J:K.63, J:T.64, J:T.64, J:T.64, J:K.227 Salt bridges: K:R.178, K:R.178 ATP.4: 15 residues within 4Å: Chain K: D.21, V.22, G.23, P.62, P.63, G.64, T.65, G.66, K.67, T.68, M.69, T.166, I.200, G.228, A.229 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:G.23, K:G.64, K:T.65, K:G.66, K:K.67, K:T.68, K:M.69 Salt bridges: K:K.67, K:K.67

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

ADP.5: 14 residues within 4Å: Chain L: I.18, G.20, G.60, T.61, G.62, K.63, T.64, L.65, I.195, I.198, H.199, G.223, A.224, R.227 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.60, L:T.61, L:T.61, L:G.62, L:K.63, L:T.64, L:T.64, L:T.64, L:L.65, L:R.227 ADP.6: 9 residues within 4Å: Chain M: P.52, G.53, T.54, G.55, K.56, T.57, L.58, I.188, H.192 5 PLIP interactions: 5 interactions with chain M Hydrogen bonds: M:G.53, M:T.54, M:G.55, M:K.56, M:T.57

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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