SMTL ID : 9pjd.1

Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.67 Å

Oligo State

hetero-6-14-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK: unidentified portion of the substrate(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK.1: 17 residues within 4Å: Chain A: N.195, P.196, S.197, I.198, T.199 Chain C: Y.153, V.154, V.202 Chain D: G.152, Y.153, V.154, V.202 Chain E: G.152, Y.153, V.154, V.202 Chain F: Y.153 13 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E, 3 interactions with chain D, 2 interactions with chain F, 3 interactions with chain C Hydrophobic interactions: A:N.195, A:T.199, D:Y.153, D:V.154, F:Y.153, F:Y.153, C:V.154, C:V.202 Hydrogen bonds: A:P.196, E:G.152, E:V.154, D:V.154, C:V.154

6 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 19 residues within 4Å: Chain A: Y.77, V.78, I.79, Q.81, T.121, G.122, S.123, G.124, K.125, T.126, L.127, A.250, L.317, I.325, P.329, A.369, R.370 Chain B: E.303, R.307 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.79, A:G.122, A:S.123, A:S.123, A:G.124, A:K.125, A:T.126, A:T.126, A:T.126, A:L.127, A:R.370, B:R.307, B:R.307 Salt bridges: A:K.125, A:R.370, A:R.370 AGS.3: 22 residues within 4Å: Chain B: Y.77, V.78, I.79, Q.81, T.121, G.122, S.123, G.124, K.125, T.126, L.127, D.184, E.185, A.250, L.317, I.325, P.329, A.369, R.370 Chain C: E.303, R.307 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.79, B:T.121, B:G.122, B:S.123, B:S.123, B:S.123, B:G.124, B:K.125, B:T.126, B:L.127, B:E.185, C:R.307, C:R.307 Salt bridges: B:K.125, B:R.370, B:R.370 AGS.5: 22 residues within 4Å: Chain C: Y.77, V.78, I.79, Q.81, T.121, G.122, S.123, G.124, K.125, T.126, L.127, E.185, A.250, L.317, I.325, P.329, A.369, R.370 Chain D: E.216, E.303, R.307 Ligands: MG.6 17 PLIP interactions: 1 interactions with chain D, 16 interactions with chain C Hydrogen bonds: D:R.307, C:I.79, C:I.79, C:T.121, C:G.122, C:S.123, C:G.124, C:K.125, C:K.125, C:T.126, C:T.126, C:L.127, C:A.250, C:R.370 Salt bridges: C:K.125, C:R.370, C:R.370 AGS.7: 24 residues within 4Å: Chain D: Y.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, E.185, A.250, L.317, I.325, P.329, A.369, R.370, R.373 Chain E: E.216, E.303, R.307 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:I.79, D:G.122, D:S.123, D:S.123, D:G.124, D:K.125, D:K.125, D:T.126, D:L.127 Salt bridges: D:K.125, D:R.370, D:R.370 AGS.9: 22 residues within 4Å: Chain E: Y.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, D.184, A.250, L.317, I.325, P.329, A.369, R.370 Chain F: E.303, R.307 Ligands: MG.10 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.79, E:G.122, E:S.123, E:G.124, E:K.125, E:T.126, E:L.127, E:R.370, F:R.307, F:R.307 Salt bridges: E:K.125, E:R.370 AGS.11: 19 residues within 4Å: Chain F: V.78, I.79, Q.81, T.121, G.122, S.123, G.124, K.125, T.126, L.127, D.184, E.185, A.250, L.317, I.325, P.329, A.369, R.370 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:I.79, F:G.122, F:G.124, F:K.125, F:T.126, F:L.127, F:D.184, F:E.185, F:E.185 Salt bridges: F:R.370, F:R.370

5 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain B: T.126, D.184, E.185 Chain C: K.213, E.216, R.307 Ligands: AGS.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.126, B:D.184 MG.6: 7 residues within 4Å: Chain C: T.126, D.184, E.185, R.370 Chain D: E.216, R.307 Ligands: AGS.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.126, C:D.184 MG.8: 4 residues within 4Å: Chain D: T.126, D.184, E.185 Ligands: AGS.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.126, D:D.184 MG.10: 5 residues within 4Å: Chain E: T.126, D.184 Chain F: K.213, R.307 Ligands: AGS.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.126, E:D.184 MG.12: 4 residues within 4Å: Chain F: K.125, T.126, D.184 Ligands: AGS.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.126, F:D.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc within a translocation complex. To Be Published

Release Date

2025-11-12

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpX: ABCDEF
ATP-dependent Clp protease proteolytic subunit: GHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
Q

Q
R

R
S

S
T

T
U

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

Related Entries With Identical Sequence