SMTL ID : 8cbl.1

Structure of human mitochondrial RNase Z in complex with mitochondrial pre-tRNA-His(0,Ser)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-1-mer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 26 residues within 4Å: Chain A: G.17, S.20, G.21, L.22, D.41, L.42, S.45, A.63, D.64, V.65, C.91, A.92, G.93, V.120, T.153, A.154, S.155, Y.168, K.172, P.198, G.199, L.200, F.201, T.203, P.204, L.205 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.198, A:L.205 Hydrogen bonds: A:G.17, A:A.19, A:S.20, A:S.20, A:L.22, A:L.42, A:D.64, A:D.64, A:V.65, A:C.91, A:G.93, A:K.172, A:F.201, A:F.201, A:L.205 NAD.2: 26 residues within 4Å: Chain B: G.17, S.20, G.21, L.22, D.41, L.42, S.45, A.63, D.64, V.65, C.91, A.92, G.93, V.120, T.153, A.154, S.155, Y.168, K.172, P.198, G.199, L.200, F.201, T.203, P.204, L.205 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.198 Hydrogen bonds: B:G.17, B:S.20, B:L.22, B:L.42, B:D.64, B:V.65, B:C.91, B:G.93, B:Y.168, B:K.172, B:F.201, B:T.203, B:T.203 NAD.3: 26 residues within 4Å: Chain C: G.17, A.19, S.20, G.21, L.22, D.41, L.42, S.45, A.63, D.64, V.65, C.91, A.92, G.93, T.153, A.154, S.155, Y.168, K.172, P.198, G.199, F.201, T.203, P.204, L.205, L.206 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:P.198 Hydrogen bonds: C:G.17, C:A.19, C:S.20, C:S.20, C:L.22, C:L.42, C:D.64, C:V.65, C:A.92, C:G.93, C:K.172, C:F.201, C:T.203 NAD.4: 27 residues within 4Å: Chain D: G.17, S.20, G.21, L.22, D.41, L.42, S.45, A.63, D.64, V.65, C.91, A.92, G.93, V.120, T.153, A.154, S.155, Y.168, K.172, P.198, G.199, L.200, F.201, T.203, P.204, L.205, L.206 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.198 Hydrogen bonds: D:G.17, D:S.20, D:L.22, D:L.42, D:S.45, D:S.45, D:D.64, D:V.65, D:C.91, D:G.93, D:Y.168, D:K.172, D:F.201, D:T.203, D:T.203, D:L.205

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain E: S.500, H.551, D.666, H.724 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.551, E:H.724

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.6: 18 residues within 4Å: Chain F: L.273, T.274, A.275, I.292, G.293, F.295, D.297, Q.301, T.304, S.305, C.318, L.319, L.321, K.332, N.333, L.334, L.336, M.339 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:N.333 Hydrogen bonds: F:L.273, F:G.293, F:D.297, F:T.304, F:S.305, F:S.305, F:L.319, F:K.332, F:L.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meynier, V. et al., Structural basis for human mitochondrial tRNA maturation. Nat Commun (2024)

Release Date

2024-06-12

Peptides

3-hydroxyacyl-CoA dehydrogenase type-2: ABCD
Zinc phosphodiesterase ELAC protein 2: E
tRNA methyltransferase 10 homolog C: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

3-hydroxyacyl-CoA dehydrogenase type-2

Zinc phosphodiesterase ELAC protein 2

tRNA methyltransferase 10 homolog C

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