SMTL ID : 8p4r.1

In situ structure average of GroEL14-GroES14 complexes in Escherichia coli cytosol obtained by cryo electron tomography

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-14-mer

Ligands

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

ATP.1: 26 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, 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 22 PLIP interactions: 22 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:G.414, A:N.478, A:A.479, A:A.480, A:D.494 Water bridges: A:K.50, A:K.50, A:N.152, A:N.152 Salt bridges: A:K.50 ATP.4: 26 residues within 4Å: Chain B: 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, 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 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.31, B:D.51, B:D.51, B:G.52, 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:G.414, B:N.478, B:A.479, B:A.480, B:D.494 Water bridges: B:N.152, B:N.152 Salt bridges: B:K.50 ATP.7: 26 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, S.150, 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 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:G.31, C:D.51, C:D.51, C:G.52, C:G.87, C:T.88, C:T.89, C:T.90, C:T.90, C:T.90, C:T.90, C:S.150, C:G.414, C:N.478, C:N.478, C:A.479, C:A.480, C:D.494 Water bridges: C:K.50, C:K.50, C:N.152, C:N.152 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.89, T.90, I.149, S.150, 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 20 PLIP interactions: 20 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.90, D:T.90, D:T.90, D:T.90, D:S.150, D:G.414, D:N.478, D:A.479, D:A.480, D:D.494 Water bridges: D:N.152, D:N.152 Salt bridges: D:K.50 ATP.13: 26 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, 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 22 PLIP interactions: 22 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.90, E:T.90, E:T.90, E:T.90, E:S.150, E:G.414, E:N.478, E:A.479, E:A.480, E:D.494 Water bridges: E:K.50, E:K.50, E:N.152, E:N.152 Salt bridges: E:K.50 ATP.16: 26 residues within 4Å: Chain F: 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, 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 21 PLIP interactions: 21 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:G.414, F:N.478, F:N.478, F:A.479, F:A.480, F:D.494 Water bridges: F:N.152, F:N.152 Salt bridges: F:K.50 ATP.19: 26 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, 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 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:G.31, G:D.51, G:D.51, G:G.52, G:G.87, G:T.88, G:T.89, G:T.90, G:T.90, G:T.90, G:T.90, G:S.150, G:G.414, G:N.478, G:A.479, G:A.480, G:D.494 Water bridges: G:N.152, G:N.152 Salt bridges: G:K.50 ATP.22: 26 residues within 4Å: Chain O: 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, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.23, K.24 23 PLIP interactions: 23 interactions with chain O Hydrogen bonds: O:G.31, O:D.51, O:D.51, O:D.51, O:G.52, O:G.87, O:T.88, O:T.89, O:T.90, O:T.90, O:T.90, O:T.90, O:S.150, O:G.414, O:N.478, O:A.479, O:A.480, O:D.494 Water bridges: O:N.152, O:N.152, O:D.397, O:D.397 Salt bridges: O:K.50 ATP.25: 26 residues within 4Å: Chain P: 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, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.26, K.27 23 PLIP interactions: 23 interactions with chain P Hydrogen bonds: P:G.31, P:D.51, P:D.51, P:D.51, P:G.52, P:G.87, P:T.88, P:T.89, P:T.90, P:T.90, P:T.90, P:T.90, P:S.150, P:G.414, P:N.478, P:A.479, P:A.480, P:D.494 Water bridges: P:N.152, P:N.152, P:D.397, P:D.397 Salt bridges: P:K.50 ATP.28: 26 residues within 4Å: Chain Q: 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, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.29, K.30 23 PLIP interactions: 23 interactions with chain Q Hydrogen bonds: Q:G.31, Q:D.51, Q:D.51, Q:D.51, Q:G.52, Q:G.87, Q:T.88, Q:T.89, Q:T.90, Q:T.90, Q:T.90, Q:T.90, Q:S.150, Q:G.414, Q:N.478, Q:A.479, Q:A.480, Q:D.494 Water bridges: Q:N.152, Q:N.152, Q:D.397, Q:D.397 Salt bridges: Q:K.50 ATP.31: 26 residues within 4Å: Chain R: 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, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.32, K.33 23 PLIP interactions: 23 interactions with chain R Hydrogen bonds: R:G.31, R:D.51, R:D.51, R:D.51, R:G.52, R:G.87, R:T.88, R:T.89, R:T.90, R:T.90, R:T.90, R:T.90, R:S.150, R:G.414, R:N.478, R:A.479, R:A.480, R:D.494 Water bridges: R:N.152, R:N.152, R:D.397, R:D.397 Salt bridges: R:K.50 ATP.34: 26 residues within 4Å: Chain S: 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, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.35, K.36 24 PLIP interactions: 24 interactions with chain S Hydrogen bonds: S:G.31, S:D.51, S:D.51, S:D.51, S:G.52, S:G.87, S:T.88, S:T.89, S:T.90, S:T.90, S:T.90, S:T.90, S:S.150, S:G.414, S:N.478, S:N.478, S:A.479, S:A.480, S:D.494 Water bridges: S:N.152, S:N.152, S:D.397, S:D.397 Salt bridges: S:K.50 ATP.37: 26 residues within 4Å: Chain T: 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, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.38, K.39 23 PLIP interactions: 23 interactions with chain T Hydrogen bonds: T:G.31, T:D.51, T:D.51, T:D.51, T:G.52, T:G.87, T:T.88, T:T.89, T:T.90, T:T.90, T:T.90, T:T.90, T:S.150, T:G.414, T:N.478, T:A.479, T:A.480, T:D.494 Water bridges: T:N.152, T:N.152, T:D.397, T:D.397 Salt bridges: T:K.50 ATP.40: 26 residues within 4Å: Chain U: 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, D.397, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.41, K.42 24 PLIP interactions: 24 interactions with chain U Hydrogen bonds: U:G.31, U:D.51, U:D.51, U:D.51, U:G.52, U:G.87, U:T.88, U:T.89, U:T.90, U:T.90, U:T.90, U:T.90, U:S.150, U:G.414, U:N.478, U:A.479, U:A.480, U:D.494 Water bridges: U:N.152, U:N.152, U:D.397, U:D.397, U:D.397 Salt bridges: U: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: 4 residues within 4Å: Chain B: D.86, G.87, S.150 Ligands: ATP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.86, H2O.2, H2O.2 MG.8: 4 residues within 4Å: Chain C: D.86, G.87, S.150 Ligands: ATP.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.86, H2O.3, H2O.3 MG.11: 4 residues within 4Å: Chain D: D.86, G.87, S.150 Ligands: ATP.10 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.86, H2O.4, H2O.4 MG.14: 4 residues within 4Å: Chain E: D.86, G.87, S.150 Ligands: ATP.13 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.86, H2O.5, H2O.5 MG.17: 4 residues within 4Å: Chain F: D.86, G.87, S.150 Ligands: ATP.16 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.86, H2O.6, H2O.6 MG.20: 4 residues within 4Å: Chain G: D.86, G.87, S.150 Ligands: ATP.19 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.86, H2O.7, H2O.7 MG.23: 4 residues within 4Å: Chain O: D.86, G.87, S.150 Ligands: ATP.22 3 PLIP interactions: 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:D.86, H2O.8, H2O.9 MG.26: 4 residues within 4Å: Chain P: D.86, G.87, S.150 Ligands: ATP.25 3 PLIP interactions: 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:D.86, H2O.10, H2O.10 MG.29: 4 residues within 4Å: Chain Q: D.86, G.87, S.150 Ligands: ATP.28 3 PLIP interactions: 1 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:D.86, H2O.11, H2O.11 MG.32: 4 residues within 4Å: Chain R: D.86, G.87, S.150 Ligands: ATP.31 3 PLIP interactions: 1 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:D.86, H2O.12, H2O.12 MG.35: 4 residues within 4Å: Chain S: D.86, G.87, S.150 Ligands: ATP.34 3 PLIP interactions: 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:D.86, H2O.13, H2O.13 MG.38: 4 residues within 4Å: Chain T: D.86, G.87, S.150 Ligands: ATP.37 3 PLIP interactions: 1 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:D.86, H2O.14, H2O.14 MG.41: 4 residues within 4Å: Chain U: D.86, G.87, S.150 Ligands: ATP.40 3 PLIP interactions: 1 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:D.86, H2O.15, H2O.15

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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.29, A:K.50, A:T.89 K.6: 5 residues within 4Å: Chain B: T.29, K.50, G.52, T.89 Ligands: ATP.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:T.29, 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 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:T.29, 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 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:T.29, D:T.29, D:K.50, 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 3 PLIP interactions: 3 interactions with chain F Metal complexes: 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 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.29, G:T.29, G:K.50, G:T.89 K.24: 5 residues within 4Å: Chain O: T.29, K.50, G.52, T.89 Ligands: ATP.22 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:T.29, O:K.50, O:T.89 K.27: 5 residues within 4Å: Chain P: T.29, K.50, G.52, T.89 Ligands: ATP.25 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:T.29, P:T.29, P:K.50, P:T.89 K.30: 5 residues within 4Å: Chain Q: T.29, K.50, G.52, T.89 Ligands: ATP.28 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:T.29, Q:T.29, Q:K.50, Q:T.89 K.33: 5 residues within 4Å: Chain R: T.29, K.50, G.52, T.89 Ligands: ATP.31 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:T.29, R:T.29, R:K.50, R:T.89 K.36: 5 residues within 4Å: Chain S: T.29, K.50, G.52, T.89 Ligands: ATP.34 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:T.29, S:T.29, S:K.50, S:T.89 K.39: 5 residues within 4Å: Chain T: T.29, K.50, G.52, T.89 Ligands: ATP.37 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:T.29, T:K.50, T:T.89 K.42: 5 residues within 4Å: Chain U: T.29, K.50, G.52, T.89 Ligands: ATP.40 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:T.29, U:T.29, U:K.50, U:T.89

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: ABCDEFGOPQRSTU
Co-chaperonin GroES: HIJKLMNVWXYZ01

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

O
H

P
I

Q
J

R
K

S
L

T
M

U
N

H
O

I
P

J
Q

K
R

L
S

M
T

N
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

Chaperonin GroEL

Co-chaperonin GroES

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