SMTL ID : 9c88.1

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Translocating a Portion of a Branched-Degron DHFR Substrate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-6-14-mer

Ligands

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

ATP.1: 23 residues within 4Å: Chain B: Y.41, V.42, I.43, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, E.149, A.214, L.281, I.289, P.293, A.333, R.334, R.337 Chain C: E.180, E.267, R.271 Ligands: MG.2 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.43, B:G.86, B:S.87, B:S.87, B:G.88, B:K.89, B:T.90, B:L.91, B:E.149 Salt bridges: B:K.89, B:K.89, B:R.334, B:R.334, B:R.334, C:R.271 ATP.3: 25 residues within 4Å: Chain C: Y.41, V.42, I.43, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, D.148, E.149, K.152, A.214, L.281, I.289, P.293, A.333, R.334 Chain D: L.176, E.180, E.267, R.271 Ligands: MG.4 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.43, C:G.86, C:S.87, C:S.87, C:G.88, C:K.89, C:T.90, C:L.91 Salt bridges: C:K.89, C:K.89, C:K.152, C:R.334, C:R.334, D:R.271, D:R.271 ATP.5: 25 residues within 4Å: Chain D: Y.41, V.42, I.43, Q.45, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, E.149, G.213, A.214, L.281, I.289, P.293, A.333, R.334 Chain E: L.176, E.180, E.267, R.271 Ligands: MG.6 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:I.43, D:T.85, D:G.86, D:S.87, D:S.87, D:G.88, D:K.89, D:T.90, D:L.91, D:E.149, D:A.214, E:E.267, E:E.267 Salt bridges: D:K.89, D:K.89, D:K.152, D:R.334, D:R.334, D:R.334, E:R.271

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: T.90, D.148, E.149 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.90, B:D.148 MG.4: 5 residues within 4Å: Chain C: T.90, D.148, E.149 Chain D: R.271 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.90, C:D.148 MG.6: 5 residues within 4Å: Chain D: T.90, D.148, E.149, R.334 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.90, D:D.148 MG.8: 3 residues within 4Å: Chain E: T.90, D.148 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.90

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

ADP.7: 19 residues within 4Å: Chain E: Y.41, V.42, I.43, Q.45, T.85, G.86, S.87, G.88, K.89, T.90, L.91, L.281, I.289, P.293, A.333, R.334 Chain F: E.180, R.271 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:I.43, E:I.43, E:T.85, E:G.86, E:S.87, E:G.88, E:K.89, E:T.90, E:T.90, E:L.91 Salt bridges: E:K.89, E:R.334, E:R.334 ADP.9: 17 residues within 4Å: Chain F: V.42, I.43, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, Y.146, D.148, L.281, I.289, P.293, A.333, R.334 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:I.43, F:P.84, F:G.86, F:S.87, F:G.88, F:K.89, F:T.90, F:T.90, F:L.91 Salt bridges: F:K.89, F:R.334 ADP.10: 16 residues within 4Å: Chain G: Y.41, V.42, I.43, Q.45, T.85, G.86, S.87, G.88, K.89, T.90, L.91, E.94, D.148, L.281, I.289, R.334 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:I.43, G:I.43, G:G.88, G:K.89, G:T.90, G:T.90, G:L.91, G:R.334 Salt bridges: G:K.89, G:K.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., A proteolytic AAA+ machine poised to unfold protein substrates. Nat Commun (2024)

Release Date

2024-10-16

Peptides

Branched-Degron DHFR: A
ATP-dependent Clp protease ATP-binding subunit ClpX: BCDEFG
ATP-dependent Clp protease proteolytic subunit: HIJKLMNOPQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
A

C
B

D
C

E
D

F
E

G
F

H
h

I
i

J
j

K
k

L
l

M
m

N
n

O
p

P
q

Q
r

R
s

S
t

T
u

U
v

Branched-Degron DHFR

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

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