› 4v19

Electron Microscopy
3.4Å resolution

Structure of the large subunit of the mammalian mitoribosome, part 1 of 2

Released:
DOI: 10.2210/pdb4v19/pdb
PDB entry 4v19 coloured by chain, front view.
PDB entry 4v19 coloured by chain, side view.
PDB entry 4v19 coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
The complete structure of the large subunit of the mammalian mitochondrial ribosome.
Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N
Nature 515 283-6 (2014)
PMID: 25271403
Related structures: EMD-2787

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-236647 (preferred)
Entry contents:
28 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (31 distinct):
39S ribosomal protein L27, mitochondrial Chain: 0
Molecule details ›
Chain: 0
Length: 148 amino acids
Theoretical weight: 15.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1U0F6 (Residues: 1-148; Coverage: 100%)
Gene name: MRPL27
Sequence domains: Ribosomal L27 protein
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Mitochondrial ribosomal protein L18 Chain: 1
Molecule details ›
Chain: 1
Length: 256 amino acids
Theoretical weight: 30.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0R4J8D5 (Residues: 71-97; Coverage: 17%)
Gene name: MRPL18
Large ribosomal subunit protein uL29m Chain: 2
Molecule details ›
Chain: 2
Length: 252 amino acids
Theoretical weight: 30.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SGC7 (Residues: 1-32, 33-250; Coverage: 100%)
Gene name: MRPL47
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
Large ribosomal subunit protein uL30m Chain: 3
Molecule details ›
Chain: 3
Length: 161 amino acids
Theoretical weight: 18.59 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1MIP3 (Residues: 8-161; Coverage: 96%)
Gene name: MRPL30
Sequence domains: Ribosomal protein L30p/L7e
MITORIBOSOMAL PROTEIN BL31M, MRPL55 Chain: 4
Molecule details ›
Chain: 4
Length: 126 amino acids
Theoretical weight: 15.16 KDa
Source organism: Sus scrofa
Structure domains: Mitochondrial ribosomal protein L55
Large ribosomal subunit protein bL32m Chain: 5
Molecule details ›
Chain: 5
Length: 188 amino acids
Theoretical weight: 21.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LTC4 (Residues: 20-207; Coverage: 91%)
Gene name: MRPL32
Sequence domains: Ribosomal L32p protein family
MITORIBOSOMAL PROTEIN BL33M, MRPL33 Chain: 6
Molecule details ›
Chain: 6
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Sus scrofa
Structure domains: Ribosomal protein L33
Large ribosomal subunit protein bL34m Chain: 7
Molecule details ›
Chain: 7
Length: 95 amino acids
Theoretical weight: 10.87 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: W5IDC1 (Residues: 1-95; Coverage: 100%)
Gene name: MRPL34
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35m Chain: 8
Molecule details ›
Chain: 8
Length: 188 amino acids
Theoretical weight: 21.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SVC5 (Residues: 1-79; Coverage: 83%)
Gene name: MRPL35
MITORIBOSOMAL PROTEIN BL36M, MRPL36 Chain: 9
Molecule details ›
Chain: 9
Length: 100 amino acids
Theoretical weight: 10.84 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL2 RNA-binding domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 306 amino acids
Theoretical weight: 33.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RRN2 (Residues: 1-216; Coverage: 96%)
Gene name: MRPL2
Sequence domains: Ribosomal Proteins L2, RNA binding domain
Structure domains:
MITORIBOSOMAL PROTEIN UL3M, MRPL3 Chain: E
Molecule details ›
Chain: E
Length: 348 amino acids
Theoretical weight: 38.43 KDa
Source organism: Sus scrofa
MITORIBOSOMAL PROTEIN UL4M, MRPL4 Chain: F
Molecule details ›
Chain: F
Length: 294 amino acids
Theoretical weight: 33.25 KDa
Source organism: Sus scrofa
Structure domains: Ribosomal Protein L4; Chain: A;
Large ribosomal subunit protein bL9m Chain: I
Molecule details ›
Chain: I
Length: 268 amino acids
Theoretical weight: 30.37 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LR45 (Residues: 1-268; Coverage: 100%)
Gene name: MRPL9
Sequence domains: Ribosomal protein L9, N-terminal domain
Large ribosomal subunit protein uL10m Chain: J
Molecule details ›
Chain: J
Length: 262 amino acids
Theoretical weight: 29.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RWJ0 (Residues: 10-257; Coverage: 97%)
Gene name: MRPL10
Sequence domains: Ribosomal protein L10
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL11m Chain: K
Molecule details ›
Chain: K
Length: 192 amino acids
Theoretical weight: 20.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RU54 (Residues: 1-41, 42-160; Coverage: 100%)
Gene name: MRPL11
Sequence domains: Ribosomal protein L11, RNA binding domain
Structure domains:
MITORIBOSOMAL PROTEIN UL13M, MRPL13 Chain: N
Molecule details ›
Chain: N
Length: 178 amino acids
Theoretical weight: 20.63 KDa
Source organism: Sus scrofa
Structure domains: Ribosomal protein L13
Large ribosomal subunit protein uL14m Chain: O
Molecule details ›
Chain: O
Length: 145 amino acids
Theoretical weight: 15.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RQV7 (Residues: 49-193; Coverage: 75%)
Gene name: MRPL14
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
MITORIBOSOMAL PROTEIN UL15M, MRPL15 Chain: P
Molecule details ›
Chain: P
Length: 296 amino acids
Theoretical weight: 33.48 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL16m Chain: Q
Molecule details ›
Chain: Q
Length: 251 amino acids
Theoretical weight: 28.68 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RI89 (Residues: 1-251; Coverage: 100%)
Gene name: MRPL16
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17m Chain: R
Molecule details ›
Chain: R
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RMQ4 (Residues: 1-169; Coverage: 100%)
Gene name: MRPL17
Sequence domains: Ribosomal protein L17
Mitochondrial ribosomal protein L18 Chain: S
Molecule details ›
Chain: S
Length: 180 amino acids
Theoretical weight: 20.58 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0R4J8D5 (Residues: 1-180; Coverage: 100%)
Gene name: MRPL18
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Ribosomal protein S11
Large ribosomal subunit protein bL19m Chain: T
Molecule details ›
Chain: T
Length: 292 amino acids
Theoretical weight: 33.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LNJ0 (Residues: 12-303; Coverage: 96%)
Gene name: MRPL19
Sequence domains: Ribosomal protein L19
MITORIBOSOMAL PROTEIN BL20M, MRPL20 Chain: U
Molecule details ›
Chain: U
Length: 149 amino acids
Theoretical weight: 17.55 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein bL21m Chain: V
Molecule details ›
Chain: V
Length: 209 amino acids
Theoretical weight: 23.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RY70 (Residues: 1-209; Coverage: 100%)
Sequence domains: Ribosomal prokaryotic L21 protein
MITORIBOSOMAL PROTEIN UL22M, MRPL22 Chain: W
Molecule details ›
Chain: W
Length: 210 amino acids
Theoretical weight: 24.31 KDa
Source organism: Sus scrofa
Structure domains: Ribosomal protein L22/L17
MITORIBOSOMAL PROTEIN UL23M, MRPL23 Chain: X
Molecule details ›
Chain: X
Length: 150 amino acids
Theoretical weight: 17.64 KDa
Source organism: Sus scrofa
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24m Chain: Y
Molecule details ›
Chain: Y
Length: 216 amino acids
Theoretical weight: 24.89 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RHJ1 (Residues: 1-216; Coverage: 100%)
Gene name: MRPL24
Sequence domains:
MITORIBOSOMAL 16S RRNA Chain: A
Molecule details ›
Chain: A
Length: 1570 nucleotides
Theoretical weight: 504.54 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
MITORIBOSOMAL CP TRNA Chain: B
Molecule details ›
Chain: B
Length: 62 nucleotides
Theoretical weight: 18.45 KDa
tRNA Chains: C, Z
Molecule details ›
Chains: C, Z
Length: 3 nucleotides
Theoretical weight: 895 Da

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 169 x MG
1 modified residue:
Ligand P5P 36 x P5P

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-2787

Quick links

Citations

49 review citations

Organization and Regulation of Mitochondrial Protein Synthesis.
Ott et al. (2016)
48 more

6 mentions without citation

The 55S mammalian mitochondrial ribosome and its tRNA-exit region.
Kaushal et al. (2015)
5 more