SMTL ID : 8p4m.1

CryoEM structure of a C7-symmetrical GroEL7-GroES7 cage in presence of ADP-BeFx

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-mer

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.2, BEF.3, K.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.30, A:G.32, A:G.88, A:T.89, A:T.89, A:T.90, A:T.90, A:T.91, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495 Water bridges: A:K.51, A:K.51, A:D.398 Salt bridges: A:K.51 ADP.5: 23 residues within 4Å: Chain B: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.6, BEF.7, K.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.32, B:G.88, B:G.88, B:T.89, B:T.89, B:T.90, B:T.90, B:T.91, B:G.415, B:N.479, B:A.480, B:A.481, B:D.495 Water bridges: B:K.51, B:K.51 Salt bridges: B:K.51 ADP.9: 23 residues within 4Å: Chain C: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.10, BEF.11, K.12 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.32, C:G.88, C:T.89, C:T.89, C:T.90, C:T.90, C:T.91, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495 Water bridges: C:K.51, C:K.51 Salt bridges: C:K.51 ADP.13: 23 residues within 4Å: Chain D: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.14, BEF.15, K.16 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.30, D:G.32, D:D.87, D:G.88, D:G.88, D:T.89, D:T.89, D:T.90, D:T.90, D:T.91, D:G.415, D:N.479, D:A.480, D:A.481, D:D.495 Water bridges: D:K.51, D:N.153 Salt bridges: D:K.51 ADP.17: 23 residues within 4Å: Chain E: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.18, BEF.19, K.20 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.32, E:D.87, E:D.87, E:G.88, E:G.88, E:T.89, E:T.90, E:T.90, E:T.91, E:G.415, E:N.479, E:A.480, E:A.481, E:D.495 Water bridges: E:K.51, E:K.51 Salt bridges: E:K.51 ADP.21: 23 residues within 4Å: Chain F: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.22, BEF.23, K.24 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:T.30, F:G.32, F:G.88, F:G.88, F:T.89, F:T.89, F:T.90, F:T.90, F:T.91, F:G.415, F:N.479, F:A.480, F:A.481, F:D.495 Water bridges: F:K.51, F:N.153 Salt bridges: F:K.51 ADP.25: 23 residues within 4Å: Chain G: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.26, BEF.27, K.28 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.32, G:G.88, G:T.89, G:T.89, G:T.90, G:T.90, G:T.91, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495 Water bridges: G:K.51, G:K.51 Salt bridges: G:K.51

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.87 Ligands: ADP.1, BEF.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.87, A:D.87, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: D.87 Ligands: ADP.5, BEF.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.87, B:D.87, H2O.2, H2O.2 MG.10: 3 residues within 4Å: Chain C: D.87 Ligands: ADP.9, BEF.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.87, C:D.87, H2O.3, H2O.3 MG.14: 3 residues within 4Å: Chain D: D.87 Ligands: ADP.13, BEF.15 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.87, H2O.4, H2O.4 MG.18: 3 residues within 4Å: Chain E: D.87 Ligands: ADP.17, BEF.19 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.87, H2O.5, H2O.5 MG.22: 3 residues within 4Å: Chain F: D.87 Ligands: ADP.21, BEF.23 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.87, F:D.87, H2O.6, H2O.6 MG.26: 3 residues within 4Å: Chain G: D.87 Ligands: ADP.25, BEF.27 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.87, G:D.87, H2O.7, H2O.8

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

BEF.3: 11 residues within 4Å: Chain A: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.1, MG.2, K.4 No protein-ligand interaction detected (PLIP) BEF.7: 10 residues within 4Å: Chain B: K.51, D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.5, MG.6, K.8 No protein-ligand interaction detected (PLIP) BEF.11: 10 residues within 4Å: Chain C: K.51, D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.9, MG.10, K.12 No protein-ligand interaction detected (PLIP) BEF.15: 10 residues within 4Å: Chain D: K.51, D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.13, MG.14, K.16 No protein-ligand interaction detected (PLIP) BEF.19: 10 residues within 4Å: Chain E: K.51, D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.17, MG.18, K.20 No protein-ligand interaction detected (PLIP) BEF.23: 9 residues within 4Å: Chain F: D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.21, MG.22, K.24 No protein-ligand interaction detected (PLIP) BEF.27: 11 residues within 4Å: Chain G: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.398 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.30, K.51, T.90 Ligands: ADP.1, BEF.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.30, A:K.51, A:T.90 K.8: 5 residues within 4Å: Chain B: T.30, K.51, T.90 Ligands: ADP.5, BEF.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:T.30, B:T.30, B:K.51, B:T.90 K.12: 5 residues within 4Å: Chain C: T.30, K.51, T.90 Ligands: ADP.9, BEF.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.30, C:K.51 K.16: 5 residues within 4Å: Chain D: T.30, K.51, T.90 Ligands: ADP.13, BEF.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.30, D:K.51, D:T.90 K.20: 5 residues within 4Å: Chain E: T.30, K.51, T.90 Ligands: ADP.17, BEF.19 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:T.30, E:T.30, E:K.51, E:T.90 K.24: 5 residues within 4Å: Chain F: T.30, K.51, T.90 Ligands: ADP.21, BEF.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.30, F:K.51 K.28: 5 residues within 4Å: Chain G: T.30, K.51, T.90 Ligands: ADP.25, BEF.27 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.30, G:K.51

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

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

Chaperonin GroEL

Co-chaperonin GroES

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