SMTL ID : 7swl.1

CryoEM structure of the N-terminal-deleted Rix7 AAA-ATPase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: H.318, G.320, L.322, P.360, G.361, C.362, G.363, K.364, T.365, L.366, Q.418, N.461, I.493, L.497, G.549, A.550 Chain B: D.446, R.472, R.475 Ligands: MG.3 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.320, A:G.320, A:G.361, A:C.362, A:G.363, A:K.364, A:T.365, A:L.366, A:Q.418 Salt bridges: A:K.364, A:K.364, B:R.472, B:R.472, B:R.472, B:R.475 ATP.2: 20 residues within 4Å: Chain A: D.19, I.20, A.21, S.61, G.62, C.63, G.64, K.65, T.66, T.67, N.166, I.196, L.200, G.224, S.225, Q.228 Chain B: R.150, R.177, R.178 Ligands: MG.4 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:A.21, A:A.21, A:G.62, A:C.63, A:G.64, A:K.65, A:T.66, A:T.66, A:T.67, A:N.166, A:Q.228, B:R.150, B:R.150 Salt bridges: A:K.65, A:K.65, B:R.177, B:R.177, B:R.178 ATP.5: 21 residues within 4Å: Chain B: H.318, V.319, G.320, L.322, P.360, G.361, C.362, G.363, K.364, T.365, L.366, Q.418, N.461, I.493, L.497, G.549, A.550 Chain C: D.446, R.472, R.475 Ligands: MG.7 16 PLIP interactions: 4 interactions with chain C, 12 interactions with chain B Salt bridges: C:R.472, C:R.472, C:R.472, C:R.475, B:K.364, B:K.364 Hydrogen bonds: B:G.320, B:G.320, B:G.361, B:C.362, B:G.363, B:K.364, B:T.365, B:L.366, B:Q.418, B:N.461 ATP.6: 21 residues within 4Å: Chain B: D.19, I.20, A.21, S.61, G.62, C.63, G.64, K.65, T.66, T.67, N.166, I.196, S.199, L.200, G.224, S.225, Q.228 Chain C: R.150, R.177, R.178 Ligands: MG.8 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:A.21, B:A.21, B:G.62, B:C.63, B:G.64, B:G.64, B:K.65, B:T.66, B:T.67, B:N.166, C:R.150, C:R.150, C:R.177 Salt bridges: B:K.65, B:K.65, C:R.177, C:R.178 ATP.9: 21 residues within 4Å: Chain C: H.318, V.319, G.320, L.322, P.360, G.361, C.362, G.363, K.364, T.365, L.366, Q.418, N.461, I.493, L.497, G.549, A.550 Chain D: D.446, R.472, R.475 Ligands: MG.11 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.320, C:G.320, C:G.361, C:C.362, C:G.363, C:K.364, C:T.365, C:T.365, C:L.366, C:Q.418, C:N.461 Salt bridges: C:K.364, C:K.364, D:R.472, D:R.472, D:R.472, D:R.475 ATP.10: 21 residues within 4Å: Chain C: D.19, I.20, A.21, S.61, G.62, C.63, G.64, K.65, T.66, T.67, N.166, I.196, S.199, G.224, S.225, Q.228 Chain D: D.147, R.150, R.177, R.178 Ligands: MG.12 16 PLIP interactions: 4 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:R.150, C:A.21, C:A.21, C:G.62, C:C.63, C:G.64, C:K.65, C:T.66, C:T.66, C:T.67, C:N.166 Salt bridges: D:R.177, D:R.177, D:R.178, C:K.65, C:K.65 ATP.13: 21 residues within 4Å: Chain D: H.318, V.319, G.320, L.322, P.360, G.361, C.362, G.363, K.364, T.365, L.366, Q.418, N.461, I.493, L.497, G.549, A.550 Chain E: K.349, R.472, R.475 Ligands: MG.15 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:G.320, D:G.320, D:G.361, D:C.362, D:G.363, D:K.364, D:T.365, D:T.365, D:L.366, D:Q.418, D:N.461, E:K.349, E:K.349 Salt bridges: D:K.364, D:K.364, E:R.472, E:R.472, E:R.472, E:R.475 ATP.14: 22 residues within 4Å: Chain D: D.19, I.20, A.21, S.61, G.62, C.63, G.64, K.65, T.66, T.67, N.166, I.196, S.199, L.200, G.224, S.225, Q.228 Chain E: D.147, R.150, R.177, R.178 Ligands: MG.16 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:A.21, D:A.21, D:G.62, D:C.63, D:G.64, D:K.65, D:T.66, D:T.66, D:T.67, D:N.166, D:N.166, D:S.199, D:Q.228, E:R.150, E:R.150 Salt bridges: D:K.65, D:K.65, E:R.177, E:R.177, E:R.178 ATP.18: 18 residues within 4Å: Chain E: D.19, I.20, A.21, S.61, G.62, C.63, G.64, K.65, T.66, T.67, Q.119, N.166, I.196, S.199, G.224, S.225, Q.228 Ligands: MG.19 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:A.21, E:A.21, E:G.62, E:C.63, E:G.64, E:K.65, E:T.66, E:T.67, E:Q.119, E:N.166, E:Q.228 Salt bridges: E:K.65, E:K.65

9 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.365, D.417, Q.418 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.365 MG.4: 3 residues within 4Å: Chain A: T.66, D.118 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.66 MG.7: 2 residues within 4Å: Chain B: T.365 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.365 MG.8: 3 residues within 4Å: Chain B: T.66, D.118 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.66 MG.11: 3 residues within 4Å: Chain C: T.365, D.417 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.365 MG.12: 3 residues within 4Å: Chain C: T.66, D.118 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.66 MG.15: 2 residues within 4Å: Chain D: T.365 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.365 MG.16: 3 residues within 4Å: Chain D: T.66 Chain E: D.147 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.66 MG.19: 3 residues within 4Å: Chain E: T.66, D.118 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.66

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

ADP.17: 14 residues within 4Å: Chain E: H.318, V.319, G.320, L.322, P.360, G.361, C.362, G.363, K.364, T.365, L.366, I.493, G.549, A.550 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.320, E:G.320, E:G.361, E:G.363, E:K.364, E:T.365, E:T.365, E:T.365, E:L.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kocaman, S. et al., Communication network within the essential AAA-ATPase Rix7 drives ribosome assembly. Pnas Nexus (2022)

Release Date

2022-03-02

Peptides

Rix7: ABCDEF
polyleucine: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Rix7

polyleucine