SMTL ID : 9c87.1

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-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: 25 residues within 4Å: Chain A: 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, G.213, A.214, L.281, I.289, P.293, A.333, R.334 Chain B: L.176, E.267, R.271 Ligands: MG.2 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.43, A:G.86, A:S.87, A:G.88, A:K.89, A:T.90, A:L.91, A:E.149, A:E.149, A:A.214 Salt bridges: A:K.89, A:K.89, A:K.89, A:K.152, A:R.334, A:R.334, B:R.271, B:R.271 ATP.3: 25 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, D.148, E.149, K.152, A.214, L.281, I.289, P.293, A.333, R.334 Chain C: K.177, E.180, E.267, R.271 Ligands: MG.4 18 PLIP interactions: 16 interactions with chain B, 2 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:D.148, B:E.149 Salt bridges: B:K.89, B:K.89, B:K.89, B:K.152, B:R.334, B:R.334, C:R.271, C:R.271 ATP.5: 26 residues within 4Å: Chain C: 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, 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.6 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.43, C:Q.45, C:G.86, C:S.87, C:S.87, C:G.88, C:K.89, C:T.90, C:T.90, C:L.91, C:E.149 Salt bridges: C:K.89, C:K.89, C:K.89, C:K.152, C:R.334, C:R.334, D:R.271, D:R.271

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.90, R.334 Chain B: E.180, R.271 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.90 MG.4: 5 residues within 4Å: Chain B: T.90, R.334 Chain C: E.180, R.271 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.90 MG.6: 6 residues within 4Å: Chain C: T.90, E.149, R.334 Chain D: E.180, R.271 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.90 MG.8: 4 residues within 4Å: Chain D: K.89, T.90, R.334 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.90

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

ADP.7: 19 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 Chain E: R.271 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:I.43, D:P.84, D:G.86, D:S.87, D:S.87, D:G.88, D:K.89, D:T.90, D:T.90, D:L.91 Salt bridges: D:K.89, D:R.334 ADP.9: 16 residues within 4Å: Chain E: 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, A.333, R.334 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:I.43, E:G.86 Salt bridges: E:K.89, E:R.334 ADP.10: 17 residues within 4Å: Chain F: V.42, I.43, G.44, 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 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:I.43, F:I.43, F:Q.45, 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, F:R.334

1 x MTX: METHOTREXATE(Non-covalent)

MTX.11: 21 residues within 4Å: Chain G: I.18, A.19, M.33, N.36, D.40, L.41, A.42, W.43, F.44, K.45, T.59, S.62, I.63, R.65, L.67, P.68, R.70, I.107, Y.113, T.126, F.166 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:L.41, G:L.41, G:F.44, G:K.45, G:I.63, G:I.63 Hydrogen bonds: G:I.18 Salt bridges: G:R.65, G:R.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX. 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

Related Entries With Identical Sequence