SMTL ID : 9ey2.1

Human mitochondrial RNase Z with tRNA-His-CCA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.96 Å

Oligo State

hetero-4-1-1-mer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 21 residues within 4Å: Chain E: L.221, T.222, A.223, I.240, G.241, F.243, D.245, Q.249, G.251, T.252, S.253, E.265, C.266, L.267, L.269, K.280, N.281, L.282, L.284, M.287 Chain F: A.8 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:L.221, E:T.222, E:G.241, E:G.241, E:D.245, E:G.251, E:T.252, E:S.253, E:S.253, E:L.267, E:K.280, E:L.282 Salt bridges: E:D.245

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 12 residues within 4Å: Chain F: U.1, A.66, C.67, C.68, C.69 Chain G: R.352, M.465, K.466, Q.698, K.702, D.745, R.752 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:R.352, G:D.745, G:R.752 Salt bridges: G:K.70, G:K.466, G:K.702

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain G: S.461, D.521, H.522, D.637, H.695 Ligands: ZN.4 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.521, G:H.522, G:D.637, G:D.637, G:H.695 ZN.4: 5 residues within 4Å: Chain G: H.517, H.519, H.615, D.637 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.517, G:H.519, G:H.615, G:D.637

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valentin Gese, G. et al., Structural basis of 3'-tRNA maturation by the human mitochondrial RNase Z complex. Embo J. (2024)

Release Date

2024-11-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

G
E

3-hydroxyacyl-CoA dehydrogenase type-2

tRNA methyltransferase 10 homolog C

Zinc phosphodiesterase ELAC protein 2

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