SMTL ID : 8qxu.1

In situ structure average of GroEL14-GroES7 complexes with wide GroEL7 trans ring conformation in Escherichia coli cytosol obtained by cryo electron tomography

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

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

ATP.1: 27 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, S.150, S.153, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.2, K.3 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.31, A:D.51, A:D.51, A:G.52, A:G.87, A:T.88, A:T.89, A:T.90, A:T.90, A:T.90, A:T.90, A:S.150, A:S.153, A:S.153, A:G.414, A:A.479, A:A.480, A:D.494 Water bridges: A:K.50, A:K.50, A:N.152, A:N.152, A:D.397, A:D.397, A:D.397, A:G.415, A:D.494 Salt bridges: A:K.50 ATP.4: 27 residues within 4Å: Chain B: T.29, L.30, G.31, P.32, K.50, D.51, G.52, G.85, D.86, G.87, T.88, T.89, T.90, I.149, S.153, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.5, K.6 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:G.31, B:D.51, B:D.51, B:D.51, B:G.52, B:D.86, B:G.87, B:T.88, B:T.89, B:T.90, B:T.90, B:T.90, B:T.90, B:S.150, B:S.153, B:S.153, B:G.414, B:A.479, B:A.480, B:D.494 Water bridges: B:K.50, B:K.50, B:N.152, B:N.152, B:D.397, B:G.415, B:D.494 Salt bridges: B:K.50 ATP.7: 27 residues within 4Å: Chain C: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.152, S.153, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.8, K.9 30 PLIP interactions: 30 interactions with chain C Hydrogen bonds: C:G.31, C:D.51, C:G.52, C:G.87, C:T.88, C:T.89, C:T.89, C:T.90, C:T.90, C:T.90, C:S.153, C:S.153, C:G.414, C:A.479, C:A.480, C:D.494 Water bridges: C:K.50, C:D.51, C:D.86, C:S.150, C:N.152, C:N.152, C:N.152, C:N.152, C:N.152, C:D.397, C:D.397, C:D.494, C:D.494 Salt bridges: C:K.50 ATP.10: 26 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.90, I.149, S.150, S.153, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.11, K.12 29 PLIP interactions: 29 interactions with chain D Hydrogen bonds: D:G.31, D:D.51, D:D.51, D:G.52, D:G.87, D:T.88, D:T.89, D:T.89, D:T.90, D:T.90, D:T.90, D:T.90, D:S.150, D:S.153, D:S.153, D:G.414, D:A.479, D:A.480, D:D.494 Water bridges: D:K.50, D:K.50, D:N.152, D:N.152, D:N.152, D:D.397, D:D.397, D:D.494, D:D.494 Salt bridges: D:K.50 ATP.13: 27 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, S.150, S.153, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.14, K.15 26 PLIP interactions: 26 interactions with chain E Hydrogen bonds: E:G.31, E:D.51, E:D.51, E:G.52, E:G.87, E:T.88, E:T.89, E:T.89, E:T.90, E:T.90, E:T.90, E:T.90, E:S.150, E:S.153, E:S.153, E:G.414, E:A.479, E:A.480, E:D.494 Water bridges: E:K.50, E:K.50, E:N.152, E:S.153, E:G.415, E:D.494 Salt bridges: E:K.50 ATP.16: 27 residues within 4Å: Chain F: T.29, L.30, G.31, P.32, K.50, D.51, G.52, G.85, D.86, G.87, T.88, T.89, T.90, I.149, S.153, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.17, K.18 28 PLIP interactions: 28 interactions with chain F Hydrogen bonds: F:G.31, F:D.51, F:D.51, F:G.52, F:G.87, F:T.88, F:T.89, F:T.90, F:T.90, F:T.90, F:T.90, F:S.150, F:S.153, F:S.153, F:G.414, F:A.479, F:A.480, F:D.494 Water bridges: F:K.50, F:K.50, F:N.152, F:N.152, F:S.153, F:D.397, F:D.397, F:G.415, F:G.415 Salt bridges: F:K.50 ATP.19: 28 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, S.150, N.152, S.153, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.20, K.21 27 PLIP interactions: 27 interactions with chain G Hydrogen bonds: G:G.31, G:D.51, G:D.51, G:D.51, G:G.52, G:D.86, G:G.87, G:T.88, G:T.89, G:T.89, G:T.90, G:T.90, G:T.90, G:T.90, G:S.150, G:S.153, G:D.397, G:G.414, G:A.479, G:A.480, G:D.494 Water bridges: G:K.50, G:K.50, G:N.152, G:G.415, G:D.494 Salt bridges: G:K.50

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.86, G.87, S.150 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.86, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: D.86, S.150 Ligands: ATP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.86, B:D.86, H2O.2, H2O.2 MG.8: 3 residues within 4Å: Chain C: D.86, S.150 Ligands: ATP.7 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.86, C:D.86, C:S.150, H2O.3, H2O.3 MG.11: 3 residues within 4Å: Chain D: D.86, S.150 Ligands: ATP.10 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.86, D:D.86, H2O.4, H2O.4 MG.14: 3 residues within 4Å: Chain E: D.86, S.150 Ligands: ATP.13 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.86, E:D.86, E:S.150, H2O.6, H2O.6 MG.17: 3 residues within 4Å: Chain F: D.86, G.87 Ligands: ATP.16 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.86, H2O.6, H2O.7 MG.20: 3 residues within 4Å: Chain G: D.86, G.87 Ligands: ATP.19 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.86, H2O.7, H2O.8 MG.23: 4 residues within 4Å: Chain H: D.86, I.149, S.150 Ligands: ADP.22 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.86, H:I.149, H2O.8 MG.26: 4 residues within 4Å: Chain I: D.86, I.149, S.150 Ligands: ADP.25 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.86, I:I.149, H2O.8 MG.29: 4 residues within 4Å: Chain J: D.86, I.149, S.150 Ligands: ADP.28 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.86, J:I.149, H2O.8 MG.32: 4 residues within 4Å: Chain K: D.86, I.149, S.150 Ligands: ADP.31 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.86, K:I.149, H2O.8 MG.35: 4 residues within 4Å: Chain L: D.86, I.149, S.150 Ligands: ADP.34 3 PLIP interactions: 2 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.86, L:I.149, H2O.8 MG.38: 4 residues within 4Å: Chain M: D.86, I.149, S.150 Ligands: ADP.37 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:D.86, M:I.149, H2O.9 MG.41: 4 residues within 4Å: Chain N: D.86, I.149, S.150 Ligands: ADP.40 3 PLIP interactions: 2 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:D.86, N:I.149, H2O.9

14 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: T.29, K.50, G.52, T.89 Ligands: ATP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.29, A:T.29, A:K.50, A:T.89 K.6: 6 residues within 4Å: Chain B: T.29, L.30, K.50, G.52, T.89 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.29, B:K.50, B:T.89 K.9: 5 residues within 4Å: Chain C: T.29, K.50, G.52, T.89 Ligands: ATP.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.29, C:K.50, C:T.89 K.12: 5 residues within 4Å: Chain D: T.29, K.50, G.52, T.89 Ligands: ATP.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.29, D:T.29, D:T.89 K.15: 5 residues within 4Å: Chain E: T.29, K.50, G.52, T.89 Ligands: ATP.13 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:T.29, E:T.29, E:K.50, E:T.89 K.18: 5 residues within 4Å: Chain F: T.29, K.50, G.52, T.89 Ligands: ATP.16 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:T.29, F:T.29, F:K.50, F:T.89 K.21: 5 residues within 4Å: Chain G: T.29, K.50, G.52, T.89 Ligands: ATP.19 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.29, G:T.29, G:T.89 K.24: 6 residues within 4Å: Chain H: T.29, G.31, K.50, D.51, N.152 Ligands: ADP.22 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:T.29, H:G.31, H:K.50 K.27: 6 residues within 4Å: Chain I: T.29, G.31, K.50, D.51, N.152 Ligands: ADP.25 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:T.29, I:G.31, I:K.50 K.30: 6 residues within 4Å: Chain J: T.29, G.31, K.50, D.51, N.152 Ligands: ADP.28 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:G.31, J:K.50, J:D.51 K.33: 6 residues within 4Å: Chain K: T.29, G.31, K.50, D.51, N.152 Ligands: ADP.31 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:T.29, K:G.31, K:K.50 K.36: 6 residues within 4Å: Chain L: T.29, G.31, K.50, D.51, N.152 Ligands: ADP.34 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:T.29, L:G.31, L:K.50 K.39: 6 residues within 4Å: Chain M: T.29, G.31, K.50, D.51, N.152 Ligands: ADP.37 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.29, M:G.31 K.42: 6 residues within 4Å: Chain N: T.29, G.31, K.50, D.51, N.152 Ligands: ADP.40 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:T.29, N:G.31, N:K.50

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

ADP.22: 20 residues within 4Å: Chain H: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, I.149, N.152, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.23, K.24 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:G.31, H:D.86, H:G.87, H:T.88, H:T.89, H:G.414, H:N.478, H:A.479, H:A.480, H:D.494 ADP.25: 19 residues within 4Å: Chain I: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, G.414, I.453, N.478, A.479, A.480, I.492, D.494 Ligands: MG.26, K.27 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:G.31, I:D.86, I:G.87, I:T.88, I:T.89, I:T.90, I:T.90, I:G.414, I:N.478, I:A.479, I:A.480, I:D.494 Water bridges: I:N.152 ADP.28: 21 residues within 4Å: Chain J: T.29, L.30, G.31, P.32, D.51, D.86, G.87, T.88, T.89, T.90, I.149, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.29, K.30 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:G.31, J:D.86, J:G.87, J:T.88, J:T.89, J:T.90, J:T.90, J:G.414, J:N.478, J:A.479, J:A.480, J:D.494 Water bridges: J:I.149 ADP.31: 20 residues within 4Å: Chain K: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.32, K.33 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.31, K:D.86, K:G.87, K:T.88, K:T.89, K:T.90, K:T.90, K:G.414, K:N.478, K:N.478, K:A.479, K:A.480, K:D.494 Water bridges: K:N.152 ADP.34: 21 residues within 4Å: Chain L: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, I.149, N.152, S.153, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.35, K.36 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:G.31, L:D.86, L:G.87, L:T.88, L:T.89, L:G.414, L:N.478, L:N.478, L:A.479, L:A.480, L:D.494 Water bridges: L:I.149 ADP.37: 20 residues within 4Å: Chain M: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, I.453, N.478, A.479, A.480, I.492, D.494 Ligands: MG.38, K.39 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:G.31, M:D.86, M:G.87, M:T.88, M:T.89, M:T.90, M:T.90, M:G.414, M:N.478, M:A.479, M:A.480, M:D.494 Water bridges: M:I.149, M:N.152 ADP.40: 22 residues within 4Å: Chain N: T.29, L.30, G.31, P.32, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.41, K.42 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:G.31, N:D.86, N:G.87, N:T.88, N:T.89, N:T.90, N:T.90, N:G.414, N:N.478, N:A.479, N:A.480, N:D.494 Water bridges: N:I.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, J. et al., Visualizing chaperonin function in situ by cryo-electron tomography. Nature (2024)

Release Date

2024-07-03

Peptides

Chaperonin GroEL: ABCDEFGHIJKLMN
Co-chaperonin GroES: OPQRSTU

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
O

P
P

Q
Q

R
R

S
S

T
T

U
U

Chaperonin GroEL

Co-chaperonin GroES

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