› 5aj3

Electron Microscopy
3.6Å resolution

Structure of the small subunit of the mammalian mitoribosome

Released:
DOI: 10.2210/pdb5aj3/pdb
PDB entry 5aj3 coloured by chain, front view.
PDB entry 5aj3 coloured by chain, side view.
PDB entry 5aj3 coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.
Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N
Science 348 303-8 (2015)
PMID: 25837512
Related structures: EMD-2913

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 37-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236624 (preferred)
Entry contents:
33 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (36 distinct):
Mitochondrial ribosomal protein S2 Chain: B
Molecule details ›
Chain: B
Length: 289 amino acids
Theoretical weight: 31.73 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S001 (Residues: 1-289; Coverage: 100%)
Gene name: MRPS2
Sequence domains: Ribosomal protein S2
Mitochondrial ribosomal protein S24 Chain: C
Molecule details ›
Chain: C
Length: 167 amino acids
Theoretical weight: 19.01 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1ST79 (Residues: 1-16, 17-23, 24-31, 32-40, 41-59, 60-156; Coverage: 100%)
Gene name: MRPS24
Sequence domains: Mitochondrial ribosome subunit S24
Small ribosomal subunit protein uS5m Chain: E
Molecule details ›
Chain: E
Length: 430 amino acids
Theoretical weight: 48.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SU66 (Residues: 1-430; Coverage: 100%)
Gene name: MRPS5
Sequence domains:
MITORIBOSOMAL PROTEIN BS6M, MRPS6 Chain: F
Molecule details ›
Chain: F
Length: 124 amino acids
Theoretical weight: 14.28 KDa
Source organism: Sus scrofa
Structure domains: Alpha-Beta Plaits
MITORIBOSOMAL PROTEIN US7M, MRPS7 Chain: G
Molecule details ›
Chain: G
Length: 242 amino acids
Theoretical weight: 28.15 KDa
Source organism: Sus scrofa
Mitoribosomal protein us9m, mrps9 Chain: I
Molecule details ›
Chain: I
Length: 397 amino acids
Theoretical weight: 45.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL59 (Residues: 1-397; Coverage: 100%)
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10m Chain: J
Molecule details ›
Chain: J
Length: 201 amino acids
Theoretical weight: 23.19 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RUU2 (Residues: 1-38, 39-200; Coverage: 100%)
Gene name: MRPS10
Sequence domains: Ribosomal protein S10p/S20e
MITORIBOSOMAL PROTEIN US11M, MRPS11 Chain: K
Molecule details ›
Chain: K
Length: 196 amino acids
Theoretical weight: 20.84 KDa
Source organism: Sus scrofa
Structure domains: Ribosomal protein S11
Small ribosomal subunit protein uS12m Chain: L
Molecule details ›
Chain: L
Length: 139 amino acids
Theoretical weight: 15.26 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL52 (Residues: 1-139; Coverage: 100%)
Sequence domains: Ribosomal protein S12/S23
Structure domains: Nucleic acid-binding proteins
Mitochondrial ribosomal protein S14 Chain: N
Molecule details ›
Chain: N
Length: 128 amino acids
Theoretical weight: 15.12 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL53 (Residues: 1-128; Coverage: 100%)
Gene name: MRPS14
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: Helix Hairpins
MITORIBOSOMAL PROTEIN US15M, MRPS15 Chain: O
Molecule details ›
Chain: O
Length: 239 amino acids
Theoretical weight: 27.41 KDa
Source organism: Sus scrofa
MITORIBOSOMAL PROTEIN BS16M, MRPS16 Chain: P
Molecule details ›
Chain: P
Length: 135 amino acids
Theoretical weight: 15.18 KDa
Source organism: Sus scrofa
Structure domains: S16 Ribosomal Protein; Chain: A;
28S ribosomal protein S17, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 130 amino acids
Theoretical weight: 14.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1UDM1 (Residues: 1-130; Coverage: 100%)
Gene name: MRPS17
Sequence domains: Ribosomal protein S17
Structure domains: Nucleic acid-binding proteins
Mitoribosomal protein bs18m, mrps18c Chain: R
Molecule details ›
Chain: R
Length: 143 amino acids
Theoretical weight: 16.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL54 (Residues: 1-143; Coverage: 100%)
Gene name: MRPS18C
Sequence domains: Ribosomal protein S18
MITORIBOSOMAL PROTEIN BL19M, MRPL19 Chain: T
Molecule details ›
Chain: T
Length: 14 amino acids
Theoretical weight: 1.21 KDa
Source organism: Sus scrofa
MITORIBOSOMAL PROTEIN BS21M, MRPS21 Chain: U
Molecule details ›
Chain: U
Length: 87 amino acids
Theoretical weight: 10.68 KDa
Source organism: Sus scrofa
MITORIBOSOMAL PROTEIN MS22, MRPS22 Chain: a
Molecule details ›
Chain: a
Length: 360 amino acids
Theoretical weight: 39.6 KDa
Source organism: Sus scrofa
MITORIBOSOMAL PROTEIN MS23, MRPS23 Chain: b
Molecule details ›
Chain: b
Length: 190 amino acids
Theoretical weight: 21.67 KDa
Source organism: Sus scrofa
Small ribosomal subunit protein mS25 Chain: c
Molecule details ›
Chain: c
Length: 173 amino acids
Theoretical weight: 19.95 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL55 (Residues: 1-173; Coverage: 100%)
Gene name: MRPS25
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Small ribosomal subunit protein mS26 Chain: d
Molecule details ›
Chain: d
Length: 205 amino acids
Theoretical weight: 23.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S8A5 (Residues: 1-205; Coverage: 100%)
Gene name: MRPS26
Sequence domains: Mitochondrial ribosome subunit S26
MITORIBOSOMAL PROTEIN MS27, MRPS27 Chain: e
Molecule details ›
Chain: e
Length: 336 amino acids
Theoretical weight: 28.61 KDa
Source organism: Sus scrofa
28S ribosomal protein S28, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 188 amino acids
Theoretical weight: 21.01 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL56 (Residues: 1-188; Coverage: 100%)
Gene name: MRPS28
Sequence domains: Mitochondrial ribosomal protein MRP-S35
Small ribosomal subunit protein mS29 Chain: g
Molecule details ›
Chain: g
Length: 397 amino acids
Theoretical weight: 44.92 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RLM4 (Residues: 2-55, 56-56, 57-364; Coverage: 100%)
Gene name: DAP3
Sequence domains: Mitochondrial ribosomal death-associated protein 3
Small ribosomal subunit protein mS31 Chain: h
Molecule details ›
Chain: h
Length: 387 amino acids
Theoretical weight: 44.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RME2 (Residues: 1-183, 184-232, 233-381; Coverage: 100%)
Gene name: MRPS31
Sequence domains: Mitochondrial 28S ribosomal protein S31
Small ribosomal subunit protein mS33 Chain: i
Molecule details ›
Chain: i
Length: 106 amino acids
Theoretical weight: 12.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1V2H3 (Residues: 43-148; Coverage: 72%)
Gene name: MRPS33
Sequence domains: Mitochondrial ribosomal subunit S27
MITORIBOSOMAL PROTEIN MS34, MRPS34 Chain: j
Molecule details ›
Chain: j
Length: 218 amino acids
Theoretical weight: 25.68 KDa
Source organism: Sus scrofa
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein Chain: k
Molecule details ›
Chain: k
Length: 325 amino acids
Theoretical weight: 37.1 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SG95 (Residues: 42-366; Coverage: 89%)
Gene name: MRPS35
Sequence domains: Mitochondrial ribosomal subunit protein
CHCH domain-containing protein Chain: m
Molecule details ›
Chain: m
Length: 118 amino acids
Theoretical weight: 13.56 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SZV4 (Residues: 1-118; Coverage: 100%)
Gene name: CHCHD1
Sequence domains: CHCH domain
Small ribosomal subunit protein mS38 Chain: n
Molecule details ›
Chain: n
Length: 199 amino acids
Theoretical weight: 22.87 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL57 (Residues: 1-199; Coverage: 100%)
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein mS39 Chain: o
Molecule details ›
Chain: o
Length: 692 amino acids
Theoretical weight: 62.93 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GKS8 (Residues: 1-675, 606-690; Coverage: 87%)
Gene name: PTCD3
Sequence domains: Pentatricopeptide repeat domain
Small ribosomal subunit protein mS40 Chain: p
Molecule details ›
Chain: p
Length: 258 amino acids
Theoretical weight: 29.22 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q767K8 (Residues: 1-258; Coverage: 100%)
Gene name: MRPS18B
Sequence domains: Ribosomal protein S18
UNASSIGNED HELICES Chain: s
Molecule details ›
Chain: s
Length: 16 amino acids
Theoretical weight: 1.38 KDa
Source organism: Sus scrofa
UNASSIGNED HELICES Chain: z
Molecule details ›
Chain: z
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Sus scrofa
MITORIBOSOMAL 12S RRNA Chain: A
Molecule details ›
Chain: A
Length: 962 nucleotides
Theoretical weight: 308.99 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-SITE AND A-SITE TRNA Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 64 nucleotides
Theoretical weight: 17.74 KDa
Messenger RNA Chain: X
Molecule details ›
Chain: X
Length: 13 nucleotides
Theoretical weight: 3.55 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 144 x MG
Ligand ZN 3 x ZN
Ligand GDP 1 x GDP
1 modified residue:
Ligand P5P 6 x P5P

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-2913

Quick links

Citations

68 review citations

Cancer metabolism: a therapeutic perspective.
Martinez-Outschoorn et al. (2017)
67 more

8 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)
7 more