SMTL ID : 8ba8.1

CryoEM structure of GroEL-ADP.BeF3-Rubisco.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

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

BEF.1: 9 residues within 4Å: Chain A: D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.2, MG.3, K.4 No protein-ligand interaction detected (PLIP) BEF.7: 12 residues within 4Å: Chain B: K.51, D.52, G.53, G.86, D.87, G.88, T.89, T.90, D.398 Ligands: MG.5, K.6, ADP.8 No protein-ligand interaction detected (PLIP) BEF.11: 11 residues within 4Å: Chain C: D.52, G.53, V.54, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.9, MG.10, K.12 No protein-ligand interaction detected (PLIP) BEF.13: 10 residues within 4Å: Chain D: D.52, G.53, D.87, G.88, T.89, T.90, T.91, D.398 Ligands: MG.14, ADP.16 No protein-ligand interaction detected (PLIP) BEF.17: 12 residues within 4Å: Chain E: K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, D.398 Ligands: K.18, MG.19, ADP.20 No protein-ligand interaction detected (PLIP) BEF.21: 10 residues within 4Å: Chain F: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.22, K.23, MG.24 No protein-ligand interaction detected (PLIP) BEF.27: 10 residues within 4Å: Chain G: 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)

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

ADP.2: 26 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, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: BEF.1, MG.3, K.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.32, A:G.88, A:T.89, A:T.89, A:T.89, A:T.90, A:T.90, A:T.91, A:T.91, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495, A:D.495 Salt bridges: A:K.51 ADP.8: 26 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, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.5, K.6, BEF.7 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.32, B:G.88, B:T.89, B:T.89, B:T.89, B:T.90, B:T.90, B:T.91, B:T.91, B:G.415, B:N.479, B:A.480, B:A.481, B:D.495, B:D.495 ADP.9: 26 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, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.10, BEF.11, K.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.32, C:D.87, C:G.88, C:T.89, C:T.90, C:T.91, C:T.91, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495, C:D.495 Salt bridges: C:K.51 ADP.16: 26 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, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: BEF.13, MG.14, K.15 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.32, D:D.87, D:G.88, D:T.89, D:T.89, D:T.90, D:T.90, D:T.91, D:T.91, D:G.415, D:G.416, D:N.479, D:A.480, D:A.481, D:D.495, D:D.495 Salt bridges: D:K.51 ADP.20: 26 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, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: BEF.17, K.18, MG.19 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:G.32, E:D.87, E:G.88, E:T.89, E:T.90, E:T.90, E:T.91, E:T.91, E:G.415, E:N.479, E:A.480, E:A.481, E:D.495, E:D.495 Salt bridges: E:K.51 ADP.22: 26 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, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: BEF.21, K.23, MG.24 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.32, F:D.87, F:G.88, F:T.89, F:T.90, F:T.90, F:T.91, F:T.91, F:G.415, F:N.479, F:A.480, F:A.481, F:D.495, F:D.495 Salt bridges: F:K.51 ADP.25: 26 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, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, 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:D.87, G:G.88, G:T.89, G:T.90, G:T.90, G:T.91, G:T.91, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495, G:D.495 Salt bridges: G:K.51 ADP.31: 23 residues within 4Å: Chain H: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: K.29, MG.30 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:G.32, H:D.87, H:G.88, H:G.88, H:T.90, H:T.91, H:T.91, H:G.415, H:N.479, H:A.480, H:A.481, H:D.495, H:D.495, H:D.495 ADP.32: 23 residues within 4Å: Chain I: T.30, L.31, G.32, P.33, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.154, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.33, K.34 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.32, I:G.88, I:T.89, I:T.90, I:T.90, I:T.91, I:T.91, I:G.415, I:G.415, I:N.479, I:D.495, I:D.495 ADP.35: 22 residues within 4Å: Chain J: L.31, G.32, P.33, V.54, 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, M.488, I.493, D.495 Ligands: MG.36, K.37 16 PLIP interactions: 16 interactions with chain J Hydrogen bonds: J:T.30, J:G.32, J:D.87, J:G.88, J:T.89, J:T.90, J:T.90, J:T.91, J:T.91, J:G.415, J:N.479, J:A.480, J:A.481, J:D.495, J:D.495, J:D.495 ADP.39: 23 residues within 4Å: Chain K: L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.38, K.40 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.32, K:D.87, K:G.88, K:T.89, K:T.90, K:T.90, K:T.91, K:G.415, K:G.416, K:N.479, K:A.480, K:A.481, K:D.495, K:D.495 ADP.41: 23 residues within 4Å: Chain L: T.30, L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: K.42, MG.43 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.32, L:D.87, L:G.88, L:G.88, L:T.89, L:T.90, L:T.91, L:T.91, L:G.415, L:G.416, L:N.479, L:A.480, L:A.481, L:D.495, L:D.495 ADP.46: 25 residues within 4Å: Chain M: T.30, L.31, G.32, P.33, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.44, K.45 13 PLIP interactions: 13 interactions with chain M Hydrogen bonds: M:G.32, M:G.88, M:T.90, M:T.90, M:T.91, M:T.91, M:G.415, M:G.416, M:N.479, M:A.480, M:A.481, M:D.495, M:D.495 ADP.47: 20 residues within 4Å: Chain N: L.31, G.32, P.33, D.87, G.88, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, T.482, I.493, D.495 Ligands: MG.49 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:G.32, N:G.88, N:T.91, N:T.91, N:N.479, N:A.480, N:A.481, N:D.495, N:D.495

14 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.87, S.151 Ligands: BEF.1, ADP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.5: 5 residues within 4Å: Chain B: D.87, G.88, S.151 Ligands: BEF.7, ADP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 MG.10: 5 residues within 4Å: Chain C: D.87, G.88, S.151 Ligands: ADP.9, BEF.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.87 MG.14: 6 residues within 4Å: Chain D: D.87, G.88, S.151, D.398 Ligands: BEF.13, ADP.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.87, D:D.87 MG.19: 4 residues within 4Å: Chain E: D.87, G.88 Ligands: BEF.17, ADP.20 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.87 MG.24: 6 residues within 4Å: Chain F: D.87, G.88, S.151, D.398 Ligands: BEF.21, ADP.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.87, F:D.87 MG.26: 6 residues within 4Å: Chain G: D.87, G.88, S.151, D.398 Ligands: ADP.25, BEF.27 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.87, G:D.87 MG.30: 4 residues within 4Å: Chain H: D.87, G.88, S.151 Ligands: ADP.31 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.87, H:D.87 MG.33: 3 residues within 4Å: Chain I: D.87, S.151 Ligands: ADP.32 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.87, I:D.87 MG.36: 3 residues within 4Å: Chain J: D.87, S.151 Ligands: ADP.35 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.87, J:D.87 MG.38: 3 residues within 4Å: Chain K: D.87, S.151 Ligands: ADP.39 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.87, K:D.87 MG.43: 4 residues within 4Å: Chain L: D.87, G.88, S.151 Ligands: ADP.41 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.87, L:D.87 MG.44: 3 residues within 4Å: Chain M: D.87, S.151 Ligands: ADP.46 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.87, M:D.87 MG.49: 3 residues within 4Å: Chain N: D.87, S.151 Ligands: ADP.47 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.87, N:D.87

14 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: T.30, L.31, K.51, G.53, T.90 Ligands: BEF.1, ADP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.30, A:K.51, A:T.90 K.6: 7 residues within 4Å: Chain B: T.30, L.31, K.51, G.53, T.90 Ligands: BEF.7, ADP.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.30, B:K.51, B:T.90 K.12: 8 residues within 4Å: Chain C: T.30, L.31, K.51, D.52, G.53, T.90 Ligands: ADP.9, BEF.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.30, C:K.51, C:T.90 K.15: 6 residues within 4Å: Chain D: T.30, L.31, K.51, G.53, T.90 Ligands: ADP.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.30, D:K.51 K.18: 8 residues within 4Å: Chain E: T.30, L.31, K.51, D.52, G.53, T.90 Ligands: BEF.17, ADP.20 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.30, E:K.51, E:T.90 K.23: 7 residues within 4Å: Chain F: T.30, L.31, K.51, G.53, T.90 Ligands: BEF.21, ADP.22 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.30, F:K.51, F:T.90 K.28: 7 residues within 4Å: Chain G: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.25, BEF.27 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.30, G:K.51, G:T.90 K.29: 4 residues within 4Å: Chain H: T.30, G.32, K.51 Ligands: ADP.31 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.30, H:G.32 K.34: 4 residues within 4Å: Chain I: T.30, G.32, K.51 Ligands: ADP.32 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:G.32 K.37: 5 residues within 4Å: Chain J: T.30, G.32, G.35, K.51 Ligands: ADP.35 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.30, J:G.32 K.40: 4 residues within 4Å: Chain K: T.30, G.32, K.51 Ligands: ADP.39 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:T.30, K:G.32 K.42: 4 residues within 4Å: Chain L: T.30, G.32, K.51 Ligands: ADP.41 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:G.32 K.45: 4 residues within 4Å: Chain M: T.30, G.32, K.51 Ligands: ADP.46 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.30, M:G.32 K.48: 5 residues within 4Å: Chain N: T.30, G.32, G.35, K.51, D.52 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:T.30, N:G.32, N:K.51

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

Chaperonin GroEL: ABCDEFGHIJKLMN

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

Chaperonin GroEL

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