SMTL ID : 8xoo.1

Cryo-EM structure of the ClpC1:ClpP1P2 degradation complex in Streptomyces hawaiiensis

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-6-1-mer

Ligands

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

ATP.1: 18 residues within 4Å: Chain O: P.65, V.66, I.67, R.69, E.93, G.95, V.96, G.97, K.98, T.99, A.100, I.234, L.238, I.276 Chain P: R.190, R.216, R.217 Ligands: MG.4 18 PLIP interactions: 5 interactions with chain P, 13 interactions with chain O Hydrogen bonds: P:R.190, O:D.64, O:I.67, O:I.67, O:E.93, O:G.95, O:G.97, O:K.98, O:T.99, O:T.99, O:T.99, O:A.100 Salt bridges: P:R.216, P:R.216, P:R.216, P:R.217, O:K.98, O:K.98 ATP.2: 17 residues within 4Å: Chain O: R.393, V.394, I.395, S.431, G.432, V.433, G.434, K.435, T.436, E.437, N.543, I.607, K.614, R.648 Chain P: E.519, R.589 Ligands: MG.3 18 PLIP interactions: 15 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:I.395, O:I.395, O:G.432, O:V.433, O:G.434, O:K.435, O:T.436, O:E.437, O:N.543, O:K.614, P:E.519, P:E.519 Salt bridges: O:K.435, O:K.435, O:R.648, O:R.648, O:R.648, P:R.589 ATP.6: 19 residues within 4Å: Chain P: R.393, V.394, I.395, S.431, G.432, V.433, G.434, K.435, T.436, E.437, N.543, I.607, K.614, A.647, R.648, R.651 Chain Q: E.519, R.589 Ligands: MG.7 18 PLIP interactions: 16 interactions with chain P, 2 interactions with chain Q Hydrogen bonds: P:I.395, P:G.432, P:V.433, P:V.433, P:G.434, P:K.435, P:T.436, P:E.437, P:N.543, P:K.614, P:K.614, Q:E.519 Salt bridges: P:K.435, P:K.435, P:R.648, P:R.648, P:R.648, Q:R.589 ATP.9: 13 residues within 4Å: Chain Q: R.393, V.394, I.395, S.431, G.432, V.433, G.434, K.435, T.436, E.437, A.647, R.648 Ligands: MG.10 13 PLIP interactions: 13 interactions with chain Q Hydrogen bonds: Q:I.395, Q:G.432, Q:V.433, Q:V.433, Q:G.434, Q:K.435, Q:T.436, Q:E.437 Salt bridges: Q:K.435, Q:K.435, Q:R.648, Q:R.648, Q:R.648 ATP.12: 13 residues within 4Å: Chain R: R.393, V.394, I.395, P.430, S.431, G.432, V.433, G.434, K.435, T.436, A.647, R.648 Ligands: MG.13 11 PLIP interactions: 11 interactions with chain R Hydrogen bonds: R:I.395, R:G.432, R:V.433, R:V.433, R:G.434, R:K.435, R:T.436, R:T.436 Salt bridges: R:K.435, R:R.648, R:R.648 ATP.15: 14 residues within 4Å: Chain S: R.393, I.395, P.430, S.431, G.432, V.433, G.434, K.435, T.436, E.437, I.607, A.647, R.648 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain S Hydrogen bonds: S:I.395, S:I.395, S:P.430, S:G.432, S:V.433, S:G.434, S:K.435, S:T.436, S:T.436, S:E.437 Salt bridges: S:R.648, S:R.648, S:R.648 ATP.18: 18 residues within 4Å: Chain O: R.589 Chain T: R.393, V.394, I.395, P.430, S.431, G.432, V.433, G.434, K.435, T.436, E.437, N.543, L.599, A.647, R.648, R.651 Ligands: MG.19 16 PLIP interactions: 15 interactions with chain T, 1 interactions with chain O Hydrogen bonds: T:I.395, T:G.432, T:V.433, T:V.433, T:G.434, T:K.435, T:T.436, T:E.437, T:E.437, T:R.651 Salt bridges: T:K.435, T:K.435, T:R.648, T:R.648, T:R.648, O:R.589

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain O: T.436, D.501 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.436 MG.4: 3 residues within 4Å: Chain O: T.99 Chain P: R.216 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain P: T.436, D.501 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.436 MG.10: 3 residues within 4Å: Chain Q: T.436, D.501 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.436 MG.13: 4 residues within 4Å: Chain R: S.431, G.432, R.648 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain S: T.436 Ligands: ATP.15 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain T: T.436 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.436

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

ADP.5: 15 residues within 4Å: Chain P: D.64, P.65, V.66, I.67, R.69, G.95, V.96, G.97, K.98, T.99, A.100, I.234, L.238, I.276 Chain Q: R.216 14 PLIP interactions: 12 interactions with chain P, 2 interactions with chain Q Hydrogen bonds: P:D.64, P:I.67, P:R.69, P:G.95, P:V.96, P:G.97, P:K.98, P:T.99, P:T.99, P:T.99, P:A.100 Salt bridges: P:K.98, Q:R.216, Q:R.216 ADP.8: 16 residues within 4Å: Chain Q: D.64, P.65, V.66, I.67, R.69, G.95, V.96, G.97, K.98, T.99, A.100, I.234, L.238, I.276 Chain R: R.190, R.216 14 PLIP interactions: 4 interactions with chain R, 10 interactions with chain Q Hydrogen bonds: R:R.190, Q:D.64, Q:I.67, Q:R.69, Q:G.95, Q:K.98, Q:T.99, Q:T.99, Q:T.99, Q:A.100 Salt bridges: R:R.190, R:R.216, R:R.216, Q:K.98 ADP.11: 16 residues within 4Å: Chain R: D.64, P.65, V.66, I.67, R.69, G.95, V.96, G.97, K.98, T.99, A.100, I.234, L.238, P.272, I.276 Chain S: R.216 11 PLIP interactions: 9 interactions with chain R, 2 interactions with chain S Hydrogen bonds: R:D.64, R:I.67, R:I.67, R:G.95, R:K.98, R:T.99, R:T.99, R:T.99 Salt bridges: R:K.98, S:R.216, S:R.216 ADP.14: 17 residues within 4Å: Chain S: D.64, P.65, V.66, I.67, R.69, E.93, P.94, G.95, V.96, G.97, K.98, T.99, A.100, I.234, L.238, D.273 Chain T: R.216 14 PLIP interactions: 12 interactions with chain S, 2 interactions with chain T Hydrogen bonds: S:D.64, S:I.67, S:R.69, S:G.95, S:V.96, S:G.97, S:K.98, S:T.99, S:T.99, S:T.99, S:A.100, T:R.216 Salt bridges: S:K.98, T:R.216 ADP.17: 15 residues within 4Å: Chain O: R.216 Chain T: D.64, P.65, V.66, R.69, P.94, G.95, V.96, G.97, K.98, T.99, A.100, I.234, P.272, I.276 12 PLIP interactions: 2 interactions with chain O, 10 interactions with chain T Salt bridges: O:R.216, O:R.216, T:K.98 Hydrogen bonds: T:D.64, T:I.67, T:G.95, T:G.97, T:K.98, T:T.99, T:T.99, T:T.99, T:A.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., Structural insights into the Clp protein degradation machinery. Mbio (2024)

Release Date

2024-03-27

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFG
ATP-dependent Clp protease proteolytic subunit: HIJKLMN
NDP-hexose 4-ketoreductase: OPQRST
casein: U

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
N

O
R

P
Q

Q
P

R
O

S
T

T
S

U
X

ATP-dependent Clp protease proteolytic subunit

ATP-dependent Clp protease proteolytic subunit

NDP-hexose 4-ketoreductase

casein

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