SMTL ID : 8qxs.1

CryoEM structure of a GroEL14-GroES7 complex in presence of ADP-BeFx with wide GroEL7 trans ring conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.2, BEF.3, K.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.31, A:G.87, A:T.88, A:T.89, A:T.89, A:T.90, A:G.414, A:N.478, A:A.479, A:A.480, A:D.494 Salt bridges: A:K.50 ADP.5: 23 residues within 4Å: Chain B: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.6, BEF.7, K.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.31, B:G.87, B:T.88, B:T.89, B:T.89, B:T.90, B:G.414, B:N.478, B:A.479, B:A.480, B:D.494 Salt bridges: B:K.50 ADP.9: 23 residues within 4Å: Chain C: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.10, BEF.11, K.12 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.31, C:D.86, C:D.86, C:G.87, C:T.88, C:T.89, C:T.89, C:T.90, C:G.414, C:N.478, C:A.479, C:A.480, C:D.494 Water bridges: C:D.86 Salt bridges: C:K.50 ADP.13: 22 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.14, BEF.15, K.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.31, D:D.86, D:D.86, D:G.87, D:T.88, D:T.89, D:T.89, D:T.90, D:G.414, D:N.478, D:A.479, D:A.480, D:D.494 Water bridges: D:D.86 Salt bridges: D:K.50 ADP.17: 23 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.18, BEF.19, K.20 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:G.31, E:D.86, E:D.86, E:G.87, E:T.88, E:T.89, E:T.89, E:T.90, E:G.414, E:N.478, E:A.479, E:A.480, E:D.494 Water bridges: E:D.86 Salt bridges: E:K.50 ADP.21: 23 residues within 4Å: Chain F: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.22, BEF.23, K.24 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.31, F:G.87, F:T.88, F:T.89, F:T.89, F:T.90, F:G.414, F:N.478, F:A.479, F:A.480, F:D.494 Water bridges: F:D.86 Salt bridges: F:K.50 ADP.25: 23 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.26, BEF.27, K.28 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:G.31, G:G.87, G:T.88, G:T.89, G:T.89, G:T.90, G:G.414, G:N.478, G:A.479, G:A.480, G:D.494 Water bridges: G:D.86 Salt bridges: G:K.50 ADP.29: 19 residues within 4Å: Chain H: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.30, K.31 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:G.31, H:D.86, H:G.87, H:T.88, H:T.88, H:T.89, H:T.90, H:G.414, H:N.478, H:A.479, H:A.480, H:D.494 ADP.32: 18 residues within 4Å: Chain I: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.33, K.34 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.31, I:D.86, I:G.87, I:T.88, I:T.88, I:T.89, I:T.90, I:G.414, I:N.478, I:A.479, I:A.480, I:D.494 ADP.35: 18 residues within 4Å: Chain J: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.36, K.37 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:G.31, J:D.86, J:G.87, J:T.88, J:T.88, J:T.89, J:T.90, J:G.414, J:N.478, J:A.479, J:A.480, J:D.494 ADP.38: 18 residues within 4Å: Chain K: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.39, K.40 11 PLIP interactions: 11 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:G.414, K:N.478, K:A.479, K:A.480, K:D.494 ADP.41: 18 residues within 4Å: Chain L: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.42, K.43 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.31, L:D.86, L:G.87, L:T.88, L:T.88, L:T.89, L:T.90, L:G.414, L:N.478, L:A.479, L:D.494 ADP.44: 18 residues within 4Å: Chain M: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.45, K.46 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:G.31, M:D.86, M:G.87, M:T.88, M:T.88, M:T.89, M:T.90, M:G.414, M:N.478, M:A.479, M:A.480, M:D.494 ADP.47: 18 residues within 4Å: Chain N: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.48, K.49 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:G.31, N:D.86, N:G.87, N:T.88, N:T.88, N:T.89, N:T.90, N:G.414, N:N.478, N:A.479, N:A.480, N:D.494

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.86 Ligands: ADP.1, BEF.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.86, A:D.86, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: D.86 Ligands: ADP.5, BEF.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.86, H2O.1, H2O.1 MG.10: 3 residues within 4Å: Chain C: D.86 Ligands: ADP.9, BEF.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.86, C:D.86, H2O.1, H2O.1 MG.14: 3 residues within 4Å: Chain D: D.86 Ligands: ADP.13, BEF.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.86, D:D.86, H2O.1, H2O.1 MG.18: 3 residues within 4Å: Chain E: D.86 Ligands: ADP.17, BEF.19 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.86, E:D.86, H2O.1, H2O.1 MG.22: 3 residues within 4Å: Chain F: D.86 Ligands: ADP.21, BEF.23 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.86, H2O.1, H2O.1 MG.26: 3 residues within 4Å: Chain G: D.86 Ligands: ADP.25, BEF.27 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.86, H2O.1, H2O.1 MG.30: 2 residues within 4Å: Chain H: D.86 Ligands: ADP.29 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.86, H:D.86, H2O.1 MG.33: 2 residues within 4Å: Chain I: D.86 Ligands: ADP.32 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.86, I:D.86, H2O.1 MG.36: 2 residues within 4Å: Chain J: D.86 Ligands: ADP.35 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.86, J:D.86, H2O.1 MG.39: 2 residues within 4Å: Chain K: D.86 Ligands: ADP.38 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.86, K:D.86, H2O.1 MG.42: 2 residues within 4Å: Chain L: D.86 Ligands: ADP.41 3 PLIP interactions: 2 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.86, L:D.86, H2O.1 MG.45: 2 residues within 4Å: Chain M: D.86 Ligands: ADP.44 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:D.86, M:D.86, H2O.1 MG.48: 2 residues within 4Å: Chain N: D.86 Ligands: ADP.47 3 PLIP interactions: 2 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:D.86, N:D.86, H2O.1

7 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 10 residues within 4Å: Chain A: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: ADP.1, MG.2, K.4 No protein-ligand interaction detected (PLIP) BEF.7: 9 residues within 4Å: Chain B: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: ADP.5, MG.6, K.8 No protein-ligand interaction detected (PLIP) BEF.11: 9 residues within 4Å: Chain C: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: ADP.9, MG.10, K.12 No protein-ligand interaction detected (PLIP) BEF.15: 9 residues within 4Å: Chain D: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: ADP.13, MG.14, K.16 No protein-ligand interaction detected (PLIP) BEF.19: 9 residues within 4Å: Chain E: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: ADP.17, MG.18, K.20 No protein-ligand interaction detected (PLIP) BEF.23: 9 residues within 4Å: Chain F: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: ADP.21, MG.22, K.24 No protein-ligand interaction detected (PLIP) BEF.27: 10 residues within 4Å: Chain G: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: ADP.25, MG.26, K.28 No protein-ligand interaction detected (PLIP)

14 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: T.29, K.50, T.89 Ligands: ADP.1, BEF.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.29, A:K.50 K.8: 5 residues within 4Å: Chain B: T.29, K.50, T.89 Ligands: ADP.5, BEF.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.29, B:K.50 K.12: 5 residues within 4Å: Chain C: T.29, K.50, T.89 Ligands: ADP.9, BEF.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.29, C:K.50 K.16: 5 residues within 4Å: Chain D: T.29, K.50, T.89 Ligands: ADP.13, BEF.15 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.29, D:K.50 K.20: 5 residues within 4Å: Chain E: T.29, K.50, T.89 Ligands: ADP.17, BEF.19 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.29, E:K.50 K.24: 5 residues within 4Å: Chain F: T.29, K.50, T.89 Ligands: ADP.21, BEF.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.29, F:K.50 K.28: 5 residues within 4Å: Chain G: T.29, K.50, T.89 Ligands: ADP.25, BEF.27 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.29, G:K.50 K.31: 4 residues within 4Å: Chain H: T.29, G.31, K.50 Ligands: ADP.29 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.29, H:G.31 K.34: 4 residues within 4Å: Chain I: T.29, G.31, K.50 Ligands: ADP.32 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:T.29, I:G.31, I:K.50 K.37: 4 residues within 4Å: Chain J: T.29, G.31, K.50 Ligands: ADP.35 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.29, J:G.31 K.40: 4 residues within 4Å: Chain K: T.29, G.31, K.50 Ligands: ADP.38 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:T.29, K:G.31, K:K.50 K.43: 4 residues within 4Å: Chain L: T.29, G.31, K.50 Ligands: ADP.41 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:T.29, L:G.31, L:K.50 K.46: 4 residues within 4Å: Chain M: T.29, G.31, K.50 Ligands: ADP.44 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.29, M:G.31 K.49: 4 residues within 4Å: Chain N: T.29, G.31, K.50 Ligands: ADP.47 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:T.29, N:G.31, N:K.50

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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