SMTL ID : 6mat.1

Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.50 Å

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: H.502, P.543, P.544, G.545, C.546, G.547, K.548, T.549, L.550, N.645 Chain B: D.630, R.656, R.659 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.545, A:C.546, A:G.547, A:K.548, A:T.549, A:T.549, A:T.549, A:L.550, A:N.645, B:D.630, B:D.630, B:R.656 Salt bridges: A:K.548, A:K.548, B:R.656, B:R.659 ATP.2: 14 residues within 4Å: Chain A: D.203, P.244, S.245, G.246, C.247, G.248, K.249, T.250, T.251, N.350, Q.412 Chain B: D.331, R.334, R.362 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.246, A:C.247, A:C.247, A:G.248, A:K.249, A:T.250, A:T.250, A:T.250, A:T.251, A:N.350, A:N.350, A:Q.412 Salt bridges: A:K.249, A:K.249, B:R.362, B:R.362, B:R.362 ATP.3: 13 residues within 4Å: Chain B: H.502, P.543, P.544, G.545, C.546, G.547, K.548, T.549, L.550, N.645 Chain C: D.630, R.656, R.659 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.545, B:C.546, B:G.547, B:K.548, B:T.549, B:T.549, B:T.549, B:L.550, B:N.645, C:D.630, C:R.656 Salt bridges: B:K.548, B:K.548, C:R.656, C:R.659 ATP.4: 14 residues within 4Å: Chain B: D.203, P.244, S.245, G.246, C.247, G.248, K.249, T.250, T.251, N.350, Q.412 Chain C: D.331, R.334, R.362 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.246, B:C.247, B:C.247, B:G.248, B:K.249, B:T.250, B:T.250, B:T.250, B:T.251, B:N.350, B:N.350, B:Q.412 Salt bridges: B:K.249, B:K.249, C:R.362, C:R.362, C:R.362 ATP.5: 13 residues within 4Å: Chain C: H.502, P.543, P.544, G.545, C.546, G.547, K.548, T.549, L.550, N.645 Chain D: D.630, R.656, R.659 16 PLIP interactions: 5 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:D.630, D:D.630, D:R.656, C:G.545, C:C.546, C:G.547, C:K.548, C:T.549, C:T.549, C:T.549, C:L.550, C:N.645 Salt bridges: D:R.656, D:R.659, C:K.548, C:K.548 ATP.6: 14 residues within 4Å: Chain C: D.203, P.244, S.245, G.246, C.247, G.248, K.249, T.250, T.251, N.350, Q.412 Chain D: D.331, R.334, R.362 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.246, C:C.247, C:C.247, C:G.248, C:K.249, C:T.250, C:T.250, C:T.250, C:T.251, C:N.350, C:N.350, C:Q.412 Salt bridges: C:K.249, C:K.249, D:R.362, D:R.362, D:R.362 ATP.7: 13 residues within 4Å: Chain D: H.502, P.543, P.544, G.545, C.546, G.547, K.548, T.549, L.550, N.645 Chain E: D.630, R.656, R.659 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:G.545, D:C.546, D:G.547, D:K.548, D:T.549, D:T.549, D:T.549, D:L.550, D:N.645, E:D.630, E:D.630, E:R.656 Salt bridges: D:K.548, D:K.548, E:R.656, E:R.659 ATP.8: 16 residues within 4Å: Chain D: D.203, P.244, S.245, G.246, C.247, G.248, K.249, T.250, T.251, N.350, G.408, S.409, Q.412 Chain E: D.331, R.334, R.362 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.246, D:C.247, D:C.247, D:G.248, D:K.249, D:T.250, D:T.250, D:T.250, D:T.251, D:N.350, D:N.350, D:Q.412 Salt bridges: D:K.249, D:K.249, E:R.362, E:R.362, E:R.362 ATP.9: 13 residues within 4Å: Chain E: D.203, P.244, S.245, G.246, C.247, G.248, K.249, T.250, T.251, N.350, G.408, S.409, Q.412 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.246, E:C.247, E:C.247, E:G.248, E:K.249, E:T.250, E:T.250, E:T.250, E:T.251, E:N.350, E:N.350 Salt bridges: E:K.249, E:K.249 ATP.10: 6 residues within 4Å: Chain F: G.545, G.547, T.549, L.550, T.680, G.733 No protein-ligand interaction detected (PLIP) ATP.11: 12 residues within 4Å: Chain A: R.361 Chain F: D.203, P.244, S.245, G.246, C.247, G.248, K.249, T.250, T.251, N.350, I.380 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.246, F:C.247, F:C.247, F:G.248, F:K.249, F:T.250, F:T.250, F:T.250, F:T.251, F:N.350, A:R.361 Salt bridges: F:K.249, F:K.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lo, Y.H. et al., Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7. Nat Commun (2019)

Release Date

2019-02-06

Peptides

Rix7 mutant: ABCDEF
unknown protein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Rix7 mutant

unknown protein

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