SMTL ID : 8v9r.1

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Branched-Degron DHFR-ssrA Substrate Bound with MTX

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-14-mer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: Y.41, V.42, I.43, G.44, Q.45, 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 B: E.267, R.271 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.43, A:G.86, A:S.87, A:S.87, A:S.87, A:G.88, A:G.88, A:K.89, A:T.90, A:T.90, A:L.91 Salt bridges: A:K.89, A:K.89, A:R.334, A:R.334, B:R.271 ATP.3: 23 residues within 4Å: Chain B: Y.41, V.42, I.43, Q.45, T.85, G.86, S.87, G.88, K.89, T.90, L.91, E.149, K.152, A.214, L.281, I.289, P.293, A.333, R.334 Chain C: E.180, E.267, R.271 Ligands: MG.4 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.43, B:I.43, B:P.84, B:T.85, B:G.86, B:S.87, B:G.88, B:K.89, B:T.90, B:L.91, B:E.149, B:R.334 Salt bridges: B:K.89, B:K.89, B:K.89, B:K.152, B:R.334, B:R.334, C:R.271 ATP.5: 25 residues within 4Å: Chain C: Y.41, V.42, I.43, G.44, Q.45, 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 Chain D: L.176, E.180, E.267, R.271 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain C, 1 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, C:E.149, C:E.149 Salt bridges: C:K.89, C:K.89, C:R.334, C:R.334, D:R.271

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.90, D.148 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.90 MG.4: 3 residues within 4Å: Chain B: T.90, D.148 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.90 MG.6: 4 residues within 4Å: Chain C: T.90, D.148, E.149 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.90, C:D.148 MG.8: 3 residues within 4Å: Chain D: T.90, D.148 Ligands: ADP.7 No protein-ligand interaction detected (PLIP)

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

ADP.7: 18 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, L.281, I.289, P.293, A.333, R.334 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:I.43, D:G.86, D:S.87, D:S.87, D:G.88, D:K.89, D:T.90, D:L.91 Salt bridges: D:K.89, D:R.334 ADP.9: 18 residues within 4Å: Chain E: Y.41, V.42, I.43, Q.45, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, D.148, L.281, I.289, P.293, A.333, R.334 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:I.43, E:G.86, E:S.87, E:S.87, E:G.88, E:K.89, E:T.90 Salt bridges: E:K.89, E:R.334, E:R.334 ADP.10: 17 residues within 4Å: Chain F: V.42, I.43, Q.45, 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 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:I.43, F:I.43, F:G.86, F:G.88, F:K.89, F:T.90, F:L.91, F:D.148 Salt bridges: F:K.89

1 x MTX: METHOTREXATE(Non-covalent)

MTX.11: 21 residues within 4Å: Chain G: I.5, A.6, A.7, M.16, M.20, D.27, L.28, W.30, F.31, K.32, T.46, S.49, I.50, R.52, L.54, P.55, R.57, I.94, Y.100, Y.111, T.113 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:L.28, G:L.28, G:F.31, G:K.32, G:I.50 Hydrogen bonds: G:I.5, G:R.52, G:R.52, G:Y.100, G:T.113, G:T.113 Salt bridges: G:D.27, G:K.32, G:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., Cryo-EM structure of a fully-engaged DHFR-ssrA substrate and the AAA+ ClpXP protease. To Be Published

Release Date

2024-10-16

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpX: ABCDEF
Dihydrofolate reductase: G
ATP-dependent Clp protease proteolytic subunit: HIJKLMNOPQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
S

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

ATP-dependent Clp protease ATP-binding subunit ClpX

Dihydrofolate reductase

ATP-dependent Clp protease proteolytic subunit

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