SMTL ID : 8p4o.1

CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-1-mer

Ligands

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

ADP.1: 22 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, 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.31, A:D.86, A:D.86, A:G.87, A:T.88, A:T.89, A:T.90, A:T.90, A:G.414, A:G.415, A:N.478, A:A.479, A:A.480, A:D.494 Water bridges: A:D.86, A:D.494 Salt bridges: A:K.50 ADP.5: 21 residues within 4Å: Chain B: T.29, 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.6, BEF.7, K.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.31, B:D.86, B:D.86, B:G.87, B:T.88, B:T.89, B:T.90, B:T.90, B:G.414, B:N.478, B:A.479, B:A.480, B:D.494 Water bridges: B:D.86, B:S.150 Salt bridges: B:K.50 ADP.9: 20 residues within 4Å: Chain C: T.29, L.30, G.31, P.32, 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 Ligands: MG.10, BEF.11, K.12 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.31, C:G.87, C:T.88, C:T.88, C:T.89, C:T.90, C:T.90, C:G.414, C:N.478, C:A.479, C:A.480 ADP.13: 22 residues within 4Å: Chain D: T.29, L.30, G.31, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.14, BEF.15, K.16 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.31, D:D.86, D:G.87, D:T.88, D:T.89, D:T.89, D:T.90, D:T.90, D:G.414, D:G.415, D:N.478, D:A.479, D:A.480, D:D.494 ADP.17: 21 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, K.50, 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.18, BEF.19, K.20 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.31, E:G.87, E:T.88, E:T.89, E:T.90, E:T.90, E:G.414, E:N.478, E:A.479, E:A.480, E:D.494 Salt bridges: E:K.50 ADP.21: 21 residues within 4Å: Chain F: T.29, 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.22, BEF.23, K.24 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.31, F:D.86, F:G.87, F:T.88, F:T.89, F:T.89, F:T.90, F:T.90, F:G.414, F:G.415, F:N.478, F:A.479, F:A.480, F:D.494 ADP.25: 22 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, 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 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:G.31, G:D.86, G:G.87, G:T.88, G:T.88, G:T.89, G:T.90, G:T.90, G:G.414, G:N.478, G:A.479, G:A.480 Water bridges: G:D.86 Salt bridges: G:K.50

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.86, D.397 Ligands: ADP.1, BEF.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: 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: 4 residues within 4Å: Chain C: D.86, S.150 Ligands: ADP.9, BEF.11 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: 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 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain F: D.86 Ligands: ADP.21, BEF.23 No protein-ligand interaction detected (PLIP) 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

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: 10 residues within 4Å: Chain B: D.51, G.52, D.86, G.87, T.88, T.89, D.397 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, T.88, T.89, D.397 Ligands: ADP.9, MG.10, K.12 No protein-ligand interaction detected (PLIP) BEF.15: 10 residues within 4Å: Chain D: D.51, G.52, D.86, G.87, T.88, T.89, D.397 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, G.87, T.88, T.89, D.397 Ligands: ADP.17, MG.18, K.20 No protein-ligand interaction detected (PLIP) BEF.23: 9 residues within 4Å: Chain F: G.52, D.86, G.87, T.88, T.89, D.397 Ligands: ADP.21, MG.22, K.24 No protein-ligand interaction detected (PLIP) BEF.27: 9 residues within 4Å: Chain G: 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)

7 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: 6 residues within 4Å: Chain C: T.29, K.50, G.52, T.89 Ligands: ADP.9, BEF.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.29, C:K.50, C:T.89 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

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: ABCDEFG
Co-chaperonin GroES: HIJKLMN
S-adenosylmethionine synthase: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
O

I
P

J
Q

K
R

L
S

M
T

N
U

O
1

Chaperonin GroEL

Co-chaperonin GroES

S-adenosylmethionine synthase

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