› 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 4v19 coloured by chain and viewed from the front.
PDB 4v19 coloured by chain and viewed from the side.
PDB 4v19 coloured by chain and viewed from the top.
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 (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)
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: F1RT79 (Residues: 1-148; Coverage: 100%)
Sequence domains: Ribosomal L27 protein
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
39S ribosomal protein L18, mitochondrial isoform 1 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
Mitochondrial ribosomal protein L47 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)
39S ribosomal protein L30, mitochondrial Chain: 3
Molecule details ›
Chain: 3
Length: 161 amino acids
Theoretical weight: 18.59 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1STE5 (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
Mitochondrial ribosomal protein L32 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%)
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
39S ribosomal protein L34, mitochondrial 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
Mitochondrial ribosomal protein L35 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
Ribosomal Proteins L2 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
39S ribosomal protein L4, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 294 amino acids
Theoretical weight: 33.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S3J8 (Residues: 29-35, 36-310; Coverage: 91%)
Gene name: MRPL4
Sequence domains: Ribosomal protein L4/L1 family
Structure domains: Ribosomal Protein L4; Chain: A;
39S ribosomal protein L9, mitochondrial 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
Mitochondrial ribosomal protein L10 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
Ribosomal protein L11 C-terminal domain-containing protein 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
Mitochondrial ribosomal protein L14 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
39S ribosomal protein L15, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 296 amino acids
Theoretical weight: 33.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RSH0 (Residues: 1-140, 141-293; Coverage: 100%)
Gene name: MRPL15
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
39S ribosomal protein L16, mitochondrial 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
39S ribosomal protein L17, mitochondrial 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
39S ribosomal protein L18, mitochondrial isoform 1 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
Mitochondrial ribosomal protein L19 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
39S ribosomal protein L21, mitochondrial isoform d 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
KOW domain-containing protein 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

47 review citations

High-Resolution Native Mass Spectrometry.
Tamara et al. (2022)
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6 mentions without citation

When a common biological role does not imply common disease outcomes: Disparate pathology linked to human mitochondrial aminoacyl-tRNA synthetases.
González-Serrano et al. (2019)
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