› 6gaz

Electron Microscopy
3.1Å resolution

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 28S ribosomal subunit.

Released:
DOI: 10.2210/pdb6gaz/pdb
PDB entry 6gaz coloured by chain, front view.
PDB entry 6gaz coloured by chain, side view.
PDB entry 6gaz coloured by chain, top view.
Source organisms:
Primary publication:
Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.
Kummer E, Leibundgut M, Rackham O, Lee RG, Boehringer D, Filipovska A, Ban N
Nature 560 263-267 (2018)
PMID: 30089917
Related structures: EMD-4369

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
PDBe Complex ID:
PDB-CPX-236634 (preferred)
Entry contents:
33 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (36 distinct):
Translation initiation factor IF-2, mitochondrial Chain: BC
Molecule details ›
Chain: BC
Length: 657 amino acids
Theoretical weight: 72.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P46199 (Residues: 78-727; Coverage: 89%)
Gene name: MTIF2
Sequence domains:
Large ribosomal subunit protein bL19m Chain: BT
Molecule details ›
Chain: BT
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
Mitochondrial ribosomal protein S2 Chain: AB
Molecule details ›
Chain: AB
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
28S ribosomal protein S24, mitochondrial Chain: AC
Molecule details ›
Chain: AC
Length: 167 amino acids
Theoretical weight: 18.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ANU4 (Residues: 1-167; Coverage: 100%)
Gene name: MRPS24
Sequence domains: Mitochondrial ribosome subunit S24
Small ribosomal subunit protein uS5m Chain: AE
Molecule details ›
Chain: AE
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:
Mitochondrial ribosomal protein S6 Chain: AF
Molecule details ›
Chain: AF
Length: 124 amino acids
Theoretical weight: 14.28 KDa
Source organism: Sus scrofa
Small ribosomal subunit protein uS7m Chain: AG
Molecule details ›
Chain: AG
Length: 242 amino acids
Theoretical weight: 28.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJ25 (Residues: 1-242; Coverage: 100%)
Gene name: MRPS7
Sequence domains: Ribosomal protein S7p/S5e
Mitochondrial ribosomal protein S9 Chain: AI
Molecule details ›
Chain: AI
Length: 397 amino acids
Theoretical weight: 45.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LU08 (Residues: 1-397; Coverage: 100%)
Gene name: MRPS9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10m Chain: AJ
Molecule details ›
Chain: AJ
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
Mitochondrial ribosomal protein S11 Chain: AK
Molecule details ›
Chain: AK
Length: 196 amino acids
Theoretical weight: 20.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJJ6 (Residues: 1-196; Coverage: 100%)
Gene name: MRPS11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12m Chain: AL
Molecule details ›
Chain: AL
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
28S ribosomal protein S14, mitochondrial Chain: AN
Molecule details ›
Chain: AN
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
Small ribosomal subunit protein uS15m Chain: AO
Molecule details ›
Chain: AO
Length: 239 amino acids
Theoretical weight: 27.41 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BMP0 (Residues: 1-266; Coverage: 90%)
Gene name: MRPS15
Sequence domains: Ribosomal protein S15
bS16m, MRPS16 Chain: AP
Molecule details ›
Chain: AP
Length: 135 amino acids
Theoretical weight: 15.18 KDa
Source organism: Sus scrofa
28S ribosomal protein S17, mitochondrial Chain: AQ
Molecule details ›
Chain: AQ
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
28S ribosomal protein S18c, mitochondrial isoform 1 Chain: AR
Molecule details ›
Chain: AR
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
28S ribosomal protein S21, mitochondrial Chain: AU
Molecule details ›
Chain: AU
Length: 87 amino acids
Theoretical weight: 10.68 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZNB3 (Residues: 1-87; Coverage: 100%)
Gene name: MRPS21
Sequence domains: Ribosomal protein S21
unassigned secondary structure elements Chain: AZ
Molecule details ›
Chain: AZ
Length: 18 amino acids
Theoretical weight: 1.3 KDa
Source organism: Sus scrofa
Mitochondrial ribosomal protein S22 Chain: Aa
Molecule details ›
Chain: Aa
Length: 382 amino acids
Theoretical weight: 43.23 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AQT5 (Residues: 1-382; Coverage: 100%)
Gene name: MRPS22
Sequence domains: Mitochondrial 28S ribosomal protein S22
Small ribosomal subunit protein mS23 conserved domain-containing protein Chain: Ab
Molecule details ›
Chain: Ab
Length: 190 amino acids
Theoretical weight: 21.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AEW3 (Residues: 17-207; Coverage: 91%)
Gene name: MRPS23
Sequence domains: Mitochondrial ribosomal protein S23
Small ribosomal subunit protein mS25 Chain: Ac
Molecule details ›
Chain: Ac
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
Progonadoliberin Chain: Ad
Molecule details ›
Chain: Ad
Length: 205 amino acids
Theoretical weight: 23.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AY01 (Residues: 54-77; Coverage: 22%)
Gene name: GNRH2
28S ribosomal protein S27, mitochondrial Chain: Ae
Molecule details ›
Chain: Ae
Length: 390 amino acids
Theoretical weight: 45.24 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LK09 (Residues: 66-466; Coverage: 84%)
Gene name: MRPS27
Sequence domains: Mitochondrial 28S ribosomal protein S27
Mitochondrial ribosomal protein S28 Chain: Af
Molecule details ›
Chain: Af
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: Ag
Molecule details ›
Chain: Ag
Length: 397 amino acids
Theoretical weight: 45.58 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1XNL0 (Residues: 14-410; Coverage: 97%)
Gene name: DAP3
Sequence domains: Mitochondrial ribosomal death-associated protein 3
mS31, MRPS31 Chain: Ah
Molecule details ›
Chain: Ah
Length: 387 amino acids
Theoretical weight: 44.09 KDa
Source organism: Sus scrofa
Small ribosomal subunit protein mS33 Chain: Ai
Molecule details ›
Chain: Ai
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
Mitochondrial ribosomal protein S34 Chain: Aj
Molecule details ›
Chain: Aj
Length: 218 amino acids
Theoretical weight: 25.84 KDa
Source organism: Sus scrofa
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein Chain: Ak
Molecule details ›
Chain: Ak
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: Am
Molecule details ›
Chain: Am
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: An
Molecule details ›
Chain: An
Length: 199 amino acids
Theoretical weight: 22.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D2A802 (Residues: 1-199; Coverage: 100%)
Gene name: AURKAIP1
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein mS39 Chain: Ao
Molecule details ›
Chain: Ao
Length: 692 amino acids
Theoretical weight: 76.47 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GKS8 (Residues: 1-546, 547-690; Coverage: 100%)
Gene name: PTCD3
Sequence domains: Pentatricopeptide repeat domain
Small ribosomal subunit protein mS40 Chain: Ap
Molecule details ›
Chain: Ap
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
12S ribosomal RNA, mitochondrial Chain: AA
Molecule details ›
Chain: AA
Length: 962 nucleotides
Theoretical weight: 308.99 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site fMet-tRNAMet, mitochondrial Chain: AV
Molecule details ›
Chain: AV
Length: 71 nucleotides
Theoretical weight: 22.66 KDa
MT-CO3 mRNA, mitochondrial Chain: AX
Molecule details ›
Chain: AX
Length: 201 nucleotides
Theoretical weight: 63.95 KDa

Ligands and Environments

7 bound ligands:
Ligand GSP 1 x GSP
Ligand MG 111 x MG
Ligand NA 1 x NA
Ligand SPM 1 x SPM
Ligand ZN 3 x ZN
Ligand FME 1 x FME
Ligand GTP 1 x GTP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-4369
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Transport of Proteins into Mitochondria.
Hansen et al. (2019)
11 more

3 mentions without citation

Translation initiation in mammalian mitochondria- a prokaryotic perspective.
Ayyub et al. (2020)
2 more