› 6i9r

Electron Microscopy
3.9Å resolution

Large subunit of the human mitochondrial ribosome in complex with Virginiamycin M and Quinupristin

Released:
DOI: 10.2210/pdb6i9r/pdb
PDB entry 6i9r coloured by chain, front view.
PDB entry 6i9r coloured by chain, side view.
PDB entry 6i9r coloured by chain, top view.
Source organisms:
Primary publication:
Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth.
Sighel D, Notarangelo M, Aibara S, Re A, Ricci G, Guida M, Soldano A, Adami V, Ambrosini C, Broso F, Rosatti EF, Longhi S, Buccarelli M, D'Alessandris QG, Giannetti S, Pacioni S, Ricci-Vitiani L, Rorbach J, Pallini R, Roulland S, Amunts A, Mancini I, Modelska A, Quattrone A
OpenAccess logo Cell Rep 35 109024 (2021)
PMID: 33910005
Related structures: EMD-4434

Function and Biology Details

Reaction catalysed: 
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
PDBe Complex ID:
PDB-CPX-108724 (preferred)
Entry contents:
51 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (53 distinct):
Large ribosomal subunit protein bL32m Chain: 0
Molecule details ›
Chain: 0
Length: 188 amino acids
Theoretical weight: 21.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYC8 (Residues: 1-188; Coverage: 100%)
Gene names: HSPC283, MRPL32
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33m Chain: 1
Molecule details ›
Chain: 1
Length: 65 amino acids
Theoretical weight: 7.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75394 (Residues: 1-65; Coverage: 100%)
Gene names: C2orf1, MRPL33
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34m Chain: 2
Large ribosomal subunit protein bL35m Chain: 3
Large ribosomal subunit protein bL36m Chain: 4
Large ribosomal subunit protein mL37 Chain: 5
Large ribosomal subunit protein mL38 Chain: 6
Large ribosomal subunit protein mL39 Chain: 7
Large ribosomal subunit protein mL40 Chain: 8
Large ribosomal subunit protein mL41 Chain: 9
Large ribosomal subunit protein uL2m Chain: D
Large ribosomal subunit protein uL3m Chain: E
Large ribosomal subunit protein uL4m Chain: F
Large ribosomal subunit protein bL9m Chain: H
Large ribosomal subunit protein uL10m Chain: I
Large ribosomal subunit protein uL11m Chain: J
Large ribosomal subunit protein uL13m Chain: K
Large ribosomal subunit protein uL14m Chain: L
Large ribosomal subunit protein uL15m Chain: M
Large ribosomal subunit protein uL16m Chain: N
Large ribosomal subunit protein bL17m Chain: O
Mitochondrial ribosomal protein L18, isoform CRA_b Chain: P
Large ribosomal subunit protein bL19m Chain: Q
Large ribosomal subunit protein bL20m Chain: R
Large ribosomal subunit protein bL21m Chain: S
Large ribosomal subunit protein uL22m Chain: T
Large ribosomal subunit protein uL23m Chain: U
Large ribosomal subunit protein uL24m Chain: V
Large ribosomal subunit protein bL27m Chain: W
Large ribosomal subunit protein bL28m Chain: X
Large ribosomal subunit protein uL29m Chain: Y
Large ribosomal subunit protein uL30m Chain: Z
Large ribosomal subunit protein mL42 Chain: a
Large ribosomal subunit protein mL43 Chain: b
Large ribosomal subunit protein mL44 Chain: c
Large ribosomal subunit protein mL45 Chain: d
Large ribosomal subunit protein mL46 Chain: e
Large ribosomal subunit protein mL48 Chain: f
Large ribosomal subunit protein mL49 Chain: g
Large ribosomal subunit protein mL50 Chain: h
Large ribosomal subunit protein mL51 Chain: i
Large ribosomal subunit protein mL52 Chain: j
Large ribosomal subunit protein mL53 Chain: k
Large ribosomal subunit protein mL54 Chain: l
Large ribosomal subunit protein mL55 Chain: m
Large ribosomal subunit protein mL63 Chain: o
Large ribosomal subunit protein mL62 Chain: p
Large ribosomal subunit protein mL64 Chain: q
Large ribosomal subunit protein mL66 Chain: r
Large ribosomal subunit protein mL65 Chain: s
Quinupristin Chain: C
16S ribosomal RNA Chain: A
tRNA Val Chain: B

Ligands and Environments

4 bound ligands:
Ligand ZN 3 x ZN
Ligand MG 134 x MG
Ligand G 1 x G
Ligand H8T 1 x H8T
5 modified residues:
Ligand 5MU 1 x 5MU
Ligand 5MC 1 x 5MC
Ligand 2MA 1 x 2MA
Ligand 2MU 1 x 2MU
Ligand MHU 1 x MHU

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.9Å
Relevant EMDB volumes: EMD-4434
Expression system: Not provided

Quick links

Citations

8 review citations

Elesclomol: a copper ionophore targeting mitochondrial metabolism for cancer therapy.
Zheng et al. (2022)
7 more

1 mention without citation

Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth.
Sighel et al. (2021)