SMTL ID : 8ba9.1

CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

7 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.1: 11 residues within 4Å: Chain A: T.29, K.50, D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: ADP.2, MG.3 No protein-ligand interaction detected (PLIP) AF3.5: 8 residues within 4Å: Chain B: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) AF3.8: 9 residues within 4Å: Chain C: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.7, ADP.9 No protein-ligand interaction detected (PLIP) AF3.12: 9 residues within 4Å: Chain D: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.10, ADP.11 No protein-ligand interaction detected (PLIP) AF3.13: 10 residues within 4Å: Chain E: D.51, G.52, V.53, D.86, G.87, T.88, T.89, D.397 Ligands: MG.14, ADP.15 No protein-ligand interaction detected (PLIP) AF3.16: 9 residues within 4Å: Chain F: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: ADP.17, MG.18 No protein-ligand interaction detected (PLIP) AF3.20: 10 residues within 4Å: Chain G: K.50, D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.19, ADP.21 No protein-ligand interaction detected (PLIP)

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

ADP.2: 23 residues within 4Å: Chain A: L.30, G.31, P.32, K.50, 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, T.481, I.492, D.494 Ligands: AF3.1, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.29, A:G.31, A:G.87, A:G.87, A:T.89, A:T.90, A:G.414, A:N.478, A:A.479, A:A.480, A:D.494, A:D.494 Salt bridges: A:K.50 ADP.4: 22 residues within 4Å: Chain B: L.30, G.31, P.32, K.50, 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: AF3.5, MG.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.31, B:G.87, B:T.88, B:T.88, B:T.88, B:T.89, B:T.90, B:G.414, B:N.478, B:A.479, B:A.480, B:D.494, B:D.494 Salt bridges: B:K.50 ADP.9: 22 residues within 4Å: Chain C: L.30, G.31, P.32, K.50, 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.7, AF3.8 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.31, C:G.87, C:G.87, C:T.88, C:T.89, C:T.89, C:T.90, C:T.90, C:G.414, C:G.415, C:N.478, C:A.479, C:A.480, C:D.494, C:D.494 Salt bridges: C:K.50 ADP.11: 24 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, I.149, S.153, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.10, AF3.12 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.31, D:G.87, D:G.87, 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, D:D.494 Salt bridges: D:K.50 ADP.15: 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: AF3.13, MG.14 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:G.31, E:G.87, E:G.87, E:T.88, E:T.89, E:T.89, E:T.90, E:T.90, E:G.414, E:G.415, E:N.478, E:A.479, E:A.480, E:D.494, E:D.494 Salt bridges: E:K.50 ADP.17: 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: AF3.16, MG.18 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.31, F:G.87, F:G.87, F:T.88, F:T.89, F:T.89, F:T.90, F:T.90, F:G.414, F:N.478, F:A.479, F:A.480, F:D.494, F:D.494 Salt bridges: F:K.50 ADP.21: 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.19, AF3.20 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:D.86, G:G.87, G:G.87, G:T.88, G:T.89, G:T.89, G:T.90, G:T.90, G:G.414, G:N.478, G:A.479, G:A.480, G:D.494, G:D.494 Salt bridges: G:K.50 ADP.22: 21 residues within 4Å: Chain H: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, S.153, G.413, G.414, G.415, I.453, N.478, A.479, A.480, I.492, D.494 Ligands: MG.23, K.24 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:G.31, H:G.87, H:T.89, H:T.89, H:T.90, H:T.90, H:G.414, H:N.478, H:A.479, H:A.480, H:D.494, H:D.494 ADP.27: 21 residues within 4Å: Chain I: L.30, G.31, P.32, 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.25, K.26 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:G.31, I:D.86, I:G.87, I:T.89, I:T.89, I:T.90, I:G.414, I:N.478, I:A.479, I:A.480 ADP.30: 21 residues within 4Å: Chain J: L.30, G.31, P.32, 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: K.28, MG.29 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.89, J:T.90, J:G.414, J:N.478, J:A.479, J:A.480, J:D.494, J:D.494 ADP.31: 21 residues within 4Å: Chain K: L.30, G.31, P.32, 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.32, K.33 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.31, K:D.86, K:G.87, K:T.88, K:T.88, K:T.89, K:T.89, K:T.90, K:T.90, K:G.414, K:N.478, K:A.479, K:A.480, K:D.494, K:D.494 ADP.34: 22 residues within 4Å: Chain L: L.30, G.31, P.32, 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, M.487, I.492, D.494 Ligands: K.35, MG.36 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.31, L:D.86, L:G.87, L:T.89, L:T.89, L:T.90, L:G.414, L:A.479, L:A.480, L:D.494, L:D.494 ADP.39: 21 residues within 4Å: Chain M: L.30, G.31, P.32, V.53, D.86, 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: K.37, MG.38 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:G.31, M:T.89, M:T.89, M:G.414, M:N.478, M:A.479, M:A.480, M:D.494, M:D.494 ADP.41: 22 residues within 4Å: Chain N: L.30, G.31, P.32, 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, M.487, I.492, D.494 Ligands: K.40, MG.42 10 PLIP interactions: 10 interactions with chain N Hydrogen bonds: N:G.31, N:G.87, N:T.89, N:T.89, N:T.90, N:T.90, N:G.414, N:N.478, N:A.479, N:A.480

14 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.86, G.87, S.150 Ligands: AF3.1, ADP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.86, A:D.86 MG.6: 4 residues within 4Å: Chain B: D.86, G.87 Ligands: ADP.4, AF3.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.86, B:D.86 MG.7: 4 residues within 4Å: Chain C: D.86, G.87 Ligands: AF3.8, ADP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 MG.10: 4 residues within 4Å: Chain D: D.86, G.87 Ligands: ADP.11, AF3.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 MG.14: 4 residues within 4Å: Chain E: D.86, G.87 Ligands: AF3.13, ADP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.86 MG.18: 4 residues within 4Å: Chain F: D.86, G.87 Ligands: AF3.16, ADP.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 MG.19: 4 residues within 4Å: Chain G: D.86, G.87 Ligands: AF3.20, ADP.21 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86 MG.23: 3 residues within 4Å: Chain H: D.86, G.87 Ligands: ADP.22 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.86, H:D.86 MG.25: 3 residues within 4Å: Chain I: D.86, G.87 Ligands: ADP.27 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.86, I:D.86 MG.29: 3 residues within 4Å: Chain J: D.86, G.87 Ligands: ADP.30 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.86, J:D.86 MG.32: 3 residues within 4Å: Chain K: D.86, G.87 Ligands: ADP.31 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.86, K:D.86 MG.36: 3 residues within 4Å: Chain L: D.86, G.87 Ligands: ADP.34 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.86, L:D.86 MG.38: 2 residues within 4Å: Chain M: D.86 Ligands: ADP.39 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.86 MG.42: 3 residues within 4Å: Chain N: D.86, G.87 Ligands: ADP.41 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.86

7 x K: POTASSIUM ION(Non-covalent)

K.24: 5 residues within 4Å: Chain H: T.29, G.31, K.50, D.51 Ligands: ADP.22 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:K.50 K.26: 4 residues within 4Å: Chain I: T.29, G.31, K.50 Ligands: ADP.27 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:G.31 K.28: 5 residues within 4Å: Chain J: T.29, G.31, K.50, N.152 Ligands: ADP.30 No protein-ligand interaction detected (PLIP) K.33: 4 residues within 4Å: Chain K: T.29, G.31, K.50 Ligands: ADP.31 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:T.29, K:G.31 K.35: 4 residues within 4Å: Chain L: T.29, G.31, K.50 Ligands: ADP.34 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:T.29, L:G.31 K.37: 5 residues within 4Å: Chain M: T.29, G.31, K.50, D.51 Ligands: ADP.39 No protein-ligand interaction detected (PLIP) K.40: 5 residues within 4Å: Chain N: T.29, G.31, P.32, K.50 Ligands: ADP.41 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:G.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gardner, S. et al., Structural basis of substrate progression through the bacterial chaperonin cycle. Proc Natl Acad Sci U S A (2023)

Release Date

2023-12-27

Peptides

60 kDa chaperonin: 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

60 kDa chaperonin

Co-chaperonin GroES

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