SMTL ID : 8xon.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-7-7-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: P.65, V.66, I.67, R.69, P.94, G.95, V.96, G.97, K.98, T.99, A.100, I.234, L.238, I.276 Chain B: R.216, R.217 Ligands: MG.3 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.64, A:I.67, A:I.67, A:G.95, A:K.98, A:T.99, A:T.99, A:A.100 Salt bridges: A:K.98, A:K.98, B:R.216, B:R.216, B:R.216, B:R.217 ATP.2: 18 residues within 4Å: Chain A: R.393, V.394, I.395, S.431, G.432, V.433, G.434, K.435, T.436, E.437, N.543, M.611, A.647, R.648, R.651 Chain B: E.519, R.589 Ligands: MG.4 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.395, A:G.432, A:V.433, A:V.433, A:G.434, A:K.435, A:T.436, A:T.436, A:E.437, A:E.437, A:N.543, A:R.651, A:R.651, B:E.519 Salt bridges: A:K.435, A:K.435, A:R.648, A:R.648, A:R.648, B:R.589 ATP.5: 18 residues within 4Å: Chain B: D.64, P.65, V.66, I.67, R.69, P.94, G.95, V.96, G.97, K.98, T.99, A.100, I.234, L.238, I.276 Chain C: R.216, R.217 Ligands: MG.7 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:D.64, B:I.67, B:R.69, B:G.95, B:G.97, B:K.98, B:T.99, B:T.99, B:A.100 Salt bridges: B:K.98, B:K.98, C:R.216, C:R.216, C:R.216, C:R.217 ATP.6: 17 residues within 4Å: Chain B: R.393, V.394, I.395, S.431, G.432, V.433, G.434, K.435, T.436, E.437, I.607, A.647, R.648, R.651 Chain C: E.519, R.589 Ligands: MG.8 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.395, B:G.432, B:V.433, B:V.433, B:G.434, B:K.435, B:T.436, B:E.437, B:E.437, B:R.651, C:E.519 Salt bridges: B:K.435, B:K.435, B:R.648, B:R.648, B:R.648, C:R.589 ATP.10: 18 residues within 4Å: Chain C: 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, I.607, R.648, R.651 Chain D: R.589 Ligands: MG.11 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.395, C:P.430, C:G.432, C:V.433, C:V.433, C:G.434, C:K.435, C:T.436, C:E.437, C:E.437, C:N.543, C:R.651 Salt bridges: C:K.435, C:K.435, C:R.648, C:R.648, C:R.648, D:R.589 ATP.13: 15 residues within 4Å: Chain D: R.393, V.394, I.395, S.431, G.432, V.433, G.434, K.435, T.436, E.437, L.599, I.607, A.647, R.648 Ligands: MG.14 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:I.395, D:Q.397, D:P.430, D:G.432, D:V.433, D:V.433, D:G.434, D:K.435, D:T.436, D:T.436, D:E.437, D:E.437 Salt bridges: D:K.435, D:K.435, D:R.648, D:R.648 ATP.16: 13 residues within 4Å: Chain E: V.394, I.395, P.430, S.431, G.432, V.433, G.434, K.435, T.436, E.437, I.607, A.647, R.648 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:I.395, E:P.430, E:G.432, E:V.433, E:V.433, E:V.433, E:G.434, E:K.435, E:T.436, E:T.436, E:E.437, E:E.437 Salt bridges: E:K.435, E:R.648, E:R.648, E:R.648 ATP.18: 19 residues within 4Å: Chain A: R.589 Chain F: 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, I.607, A.647, R.648, R.651 Ligands: MG.19 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:I.395, F:P.430, F:S.431, F:G.432, F:V.433, F:V.433, F:G.434, F:T.436, F:E.437, F:E.437, F:N.543 Salt bridges: F:K.435, F:K.435, F:R.648, F:R.648, A:R.589

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.99 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.99 MG.4: 2 residues within 4Å: Chain A: T.436 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.436 MG.7: 3 residues within 4Å: Chain B: T.99, D.163 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.99 MG.8: 3 residues within 4Å: Chain B: T.436, D.501 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.436 MG.11: 3 residues within 4Å: Chain C: T.436, D.501 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.436 MG.14: 3 residues within 4Å: Chain D: T.436, R.648 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.436 MG.19: 3 residues within 4Å: Chain A: R.589 Chain F: T.436 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.436

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

ADP.9: 17 residues within 4Å: Chain C: 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, I.276 Chain D: R.216 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.64, C:I.67, C:I.67, C:G.95, C:V.96, C:G.97, C:K.98, C:T.99, C:T.99, C:A.100 Salt bridges: C:K.98, D:R.216, D:R.216 ADP.12: 14 residues within 4Å: Chain D: 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 E: R.216 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:I.67, D:R.69, D:G.95, D:K.98, D:T.99, D:T.99, D:T.99, D:A.100 Salt bridges: D:K.98, E:R.216, E:R.216 ADP.15: 16 residues within 4Å: Chain E: D.64, P.65, V.66, I.67, R.69, E.93, P.94, V.96, G.97, K.98, T.99, A.100, I.234, P.272, I.276 Chain F: R.216 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.67, E:I.67, E:K.98, E:T.99, E:T.99, E:T.99, E:A.100 Salt bridges: E:K.98, F:R.216, F:R.216 ADP.17: 16 residues within 4Å: Chain A: R.216 Chain F: 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, P.272 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain F Hydrogen bonds: A:R.216, F:I.67, F:I.67, F:G.95, F:V.96, F:G.97, F:K.98, F:T.99, F:T.99, F:T.99, F: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

NDP-hexose 4-ketoreductase: ABCDEF
casein: G
ATP-dependent Clp protease proteolytic subunit: HIJKLMN
ATP-dependent Clp protease proteolytic subunit: OPQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
R

C
Q

D
P

E
O

F
T

G
X

H
A

I
B

J
C

K
D

L
E

M
F

N
G

O
H

P
I

Q
J

R
K

S
L

T
M

U
N

NDP-hexose 4-ketoreductase

casein

ATP-dependent Clp protease proteolytic subunit

ATP-dependent Clp protease proteolytic subunit

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