SMTL ID : 6xhj.1 (2 other biounits)

Cryo-EM structure of octadecameric TF55 (beta-only) complex from S. solfataricus bound to ATP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

18 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.101, E.503 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.101 MG.3: 3 residues within 4Å: Chain B: D.101, E.503 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.101 MG.5: 3 residues within 4Å: Chain C: D.101, E.503 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.101 MG.7: 3 residues within 4Å: Chain D: D.101, E.503 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.101 MG.9: 3 residues within 4Å: Chain E: D.101, E.503 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.101 MG.11: 3 residues within 4Å: Chain F: D.101, E.503 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.101 MG.13: 3 residues within 4Å: Chain G: D.101, E.503 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.101 MG.15: 3 residues within 4Å: Chain H: D.101, E.503 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.101 MG.17: 3 residues within 4Å: Chain I: D.101, E.503 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.101 MG.19: 3 residues within 4Å: Chain J: D.101, E.503 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.101 MG.21: 3 residues within 4Å: Chain K: D.101, E.503 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.101 MG.23: 3 residues within 4Å: Chain L: D.101, E.503 Ligands: ATP.24 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.101 MG.25: 3 residues within 4Å: Chain M: D.101, E.503 Ligands: ATP.26 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.101 MG.27: 3 residues within 4Å: Chain N: D.101, E.503 Ligands: ATP.28 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.101 MG.29: 3 residues within 4Å: Chain O: D.101, E.503 Ligands: ATP.30 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.101 MG.31: 3 residues within 4Å: Chain P: D.101, E.503 Ligands: ATP.32 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.101 MG.33: 3 residues within 4Å: Chain Q: D.101, E.503 Ligands: ATP.34 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.101 MG.35: 3 residues within 4Å: Chain R: D.101, E.503 Ligands: ATP.36 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:D.101

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

ATP.2: 15 residues within 4Å: Chain A: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.49, A:G.50, A:G.71, A:D.101, A:G.102, A:T.103, A:T.103, A:T.105, A:G.417 Salt bridges: A:K.104, A:K.104, A:K.104 ATP.4: 15 residues within 4Å: Chain B: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.49, B:G.50, B:G.71, B:D.101, B:G.102, B:T.103, B:T.103, B:T.105, B:G.417 Salt bridges: B:K.104, B:K.104, B:K.104 ATP.6: 15 residues within 4Å: Chain C: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Y.49, C:G.50, C:G.71, C:D.101, C:G.102, C:T.103, C:T.103, C:T.105, C:G.417 Salt bridges: C:K.104, C:K.104, C:K.104 ATP.8: 15 residues within 4Å: Chain D: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.49, D:G.50, D:G.71, D:D.101, D:G.102, D:T.103, D:T.103, D:T.105, D:G.417 Salt bridges: D:K.104, D:K.104, D:K.104 ATP.10: 15 residues within 4Å: Chain E: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.9 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Y.49, E:G.50, E:G.71, E:D.101, E:G.102, E:T.103, E:T.103, E:T.105, E:G.417 Salt bridges: E:K.104, E:K.104, E:K.104 ATP.12: 15 residues within 4Å: Chain F: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.11 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:Y.49, F:G.50, F:G.71, F:D.101, F:G.102, F:T.103, F:T.103, F:T.105, F:G.417 Salt bridges: F:K.104, F:K.104, F:K.104 ATP.14: 15 residues within 4Å: Chain G: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.13 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:Y.49, G:G.50, G:G.71, G:D.101, G:G.102, G:T.103, G:T.103, G:T.105, G:G.417 Salt bridges: G:K.104, G:K.104, G:K.104 ATP.16: 15 residues within 4Å: Chain H: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:Y.49, H:G.50, H:G.71, H:D.101, H:G.102, H:T.103, H:T.103, H:T.105, H:G.417 Salt bridges: H:K.104, H:K.104, H:K.104 ATP.18: 15 residues within 4Å: Chain I: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.17 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:Y.49, I:G.50, I:G.71, I:D.101, I:G.102, I:T.103, I:T.103, I:T.105, I:G.417 Salt bridges: I:K.104, I:K.104, I:K.104 ATP.20: 15 residues within 4Å: Chain J: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.19 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:Y.49, J:Y.49, J:G.50, J:G.71, J:D.101, J:G.102, J:T.103, J:T.103, J:T.103, J:G.417 Salt bridges: J:K.104, J:K.104, J:K.104 ATP.22: 15 residues within 4Å: Chain K: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.21 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:Y.49, K:Y.49, K:G.50, K:G.71, K:D.101, K:G.102, K:T.103, K:T.103, K:T.103, K:G.417 Salt bridges: K:K.104, K:K.104, K:K.104 ATP.24: 15 residues within 4Å: Chain L: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.23 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:Y.49, L:Y.49, L:G.50, L:G.71, L:D.101, L:G.102, L:T.103, L:T.103, L:T.103, L:G.417 Salt bridges: L:K.104, L:K.104, L:K.104 ATP.26: 15 residues within 4Å: Chain M: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.25 13 PLIP interactions: 13 interactions with chain M Hydrogen bonds: M:Y.49, M:Y.49, M:G.50, M:G.71, M:D.101, M:G.102, M:T.103, M:T.103, M:T.103, M:G.417 Salt bridges: M:K.104, M:K.104, M:K.104 ATP.28: 15 residues within 4Å: Chain N: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.27 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:Y.49, N:Y.49, N:G.50, N:G.71, N:D.101, N:G.102, N:T.103, N:T.103, N:T.103, N:G.417 Salt bridges: N:K.104, N:K.104, N:K.104 ATP.30: 15 residues within 4Å: Chain O: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.29 13 PLIP interactions: 13 interactions with chain O Hydrogen bonds: O:Y.49, O:Y.49, O:G.50, O:G.71, O:D.101, O:G.102, O:T.103, O:T.103, O:T.103, O:G.417 Salt bridges: O:K.104, O:K.104, O:K.104 ATP.32: 15 residues within 4Å: Chain P: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.31 13 PLIP interactions: 13 interactions with chain P Hydrogen bonds: P:Y.49, P:Y.49, P:G.50, P:G.71, P:D.101, P:G.102, P:T.103, P:T.103, P:T.103, P:G.417 Salt bridges: P:K.104, P:K.104, P:K.104 ATP.34: 15 residues within 4Å: Chain Q: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.33 13 PLIP interactions: 13 interactions with chain Q Hydrogen bonds: Q:Y.49, Q:Y.49, Q:G.50, Q:G.71, Q:D.101, Q:G.102, Q:T.103, Q:T.103, Q:T.103, Q:G.417 Salt bridges: Q:K.104, Q:K.104, Q:K.104 ATP.36: 15 residues within 4Å: Chain R: Y.49, G.50, P.51, G.71, D.101, G.102, T.103, K.104, T.105, G.416, G.417, L.486, L.488, V.501 Ligands: MG.35 13 PLIP interactions: 13 interactions with chain R Hydrogen bonds: R:Y.49, R:Y.49, R:G.50, R:G.71, R:D.101, R:G.102, R:T.103, R:T.103, R:T.103, R:G.417 Salt bridges: R:K.104, R:K.104, R:K.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, Y.C. et al., Structural analysis of the Sulfolobus solfataricus TF55beta chaperonin by cryo-electron microscopy. Acta Crystallogr.,Sect.F (2021)

Release Date

2021-03-17

Peptides

Thermosome subunit beta: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

O
A

P
A

Q
A

R
A

Thermosome subunit beta

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