› 6nf8

Electron Microscopy
3.48Å resolution

Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit -Class I

Released:
DOI: 10.2210/pdb6nf8/pdb
PDB entry 6nf8 coloured by chain, front view.
PDB entry 6nf8 coloured by chain, side view.
PDB entry 6nf8 coloured by chain, top view.
Source organisms:
Primary publication:
Structure of Human Mitochondrial Translation Initiation Factor 3 Bound to the Small Ribosomal Subunit.
Koripella RK, Sharma MR, Haque ME, Risteff P, Spremulli LL, Agrawal RK
iScience 12 76-86 (2019)
PMID: 30677741
Related structures: EMD-9362

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-215625 (preferred)
Entry contents:
31 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (32 distinct):
Small ribosomal subunit protein uS3m Chain: C
Molecule details ›
Chain: C
Length: 167 amino acids
Theoretical weight: 19.11 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2M2T7 (Residues: 1-167; 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: 47.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2KID9 (Residues: 1-430; Coverage: 100%)
Gene name: MRPS5
Sequence domains:
Small ribosomal subunit protein uS12m Chain: L
Molecule details ›
Chain: L
Length: 139 amino acids
Theoretical weight: 15.48 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q29RU1 (Residues: 1-139; Coverage: 100%)
Gene name: MRPS12
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein bS16m Chain: P
Molecule details ›
Chain: P
Length: 135 amino acids
Theoretical weight: 15.16 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82915 (Residues: 1-135; Coverage: 100%)
Gene names: MRPS16, RPMS16
Sequence domains: Ribosomal protein S16
Structure domains: S16 Ribosomal Protein; Chain: A;
Small ribosomal subunit protein uS17m Chain: Q
Molecule details ›
Chain: Q
Length: 130 amino acids
Theoretical weight: 14.5 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82916 (Residues: 1-130; Coverage: 100%)
Gene names: MRPS17, RPMS17
Sequence domains: Ribosomal protein S17
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein mS22 Chain: a
Molecule details ›
Chain: a
Length: 359 amino acids
Theoretical weight: 40.72 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82649 (Residues: 1-359; Coverage: 100%)
Gene name: MRPS22
Sequence domains: Mitochondrial 28S ribosomal protein S22
Small ribosomal subunit protein mS25 Chain: c
Molecule details ›
Chain: c
Length: 173 amino acids
Theoretical weight: 20.09 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82669 (Residues: 1-173; Coverage: 100%)
Gene names: MRPS25, RPMS25
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: 23.82 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q3SZ86 (Residues: 1-205; Coverage: 100%)
Gene name: MRPS26
Sequence domains: Mitochondrial ribosome subunit S26
Small ribosomal subunit protein mS27 Chain: e
Molecule details ›
Chain: e
Length: 415 amino acids
Theoretical weight: 48.02 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q32PI8 (Residues: 1-415; Coverage: 100%)
Gene name: MRPS27
Sequence domains: Mitochondrial 28S ribosomal protein S27
Small ribosomal subunit protein mS34 Chain: j
Molecule details ›
Chain: j
Length: 218 amino acids
Theoretical weight: 25.88 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82929 (Residues: 1-218; Coverage: 100%)
Gene name: MRPS34
Sequence domains: Mitochondrial 28S ribosomal protein S34
Small ribosomal subunit protein mS40 Chain: p
Molecule details ›
Chain: p
Length: 258 amino acids
Theoretical weight: 29.22 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82918 (Residues: 1-258; Coverage: 100%)
Gene name: MRPS18B
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS7m Chain: G
Molecule details ›
Chain: G
Length: 242 amino acids
Theoretical weight: 28.18 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q3T040 (Residues: 1-242; Coverage: 100%)
Gene name: MRPS7
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9m Chain: I
Molecule details ›
Chain: I
Length: 396 amino acids
Theoretical weight: 45.3 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q58DQ5 (Residues: 1-396; Coverage: 100%)
Gene name: MRPS9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10m Chain: J
Molecule details ›
Chain: J
Length: 201 amino acids
Theoretical weight: 23.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82670 (Residues: 1-201; Coverage: 100%)
Gene name: MRPS10
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS14m Chain: N
Molecule details ›
Chain: N
Length: 128 amino acids
Theoretical weight: 15.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q6B860 (Residues: 1-128; Coverage: 100%)
Gene name: MRPS14
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: Helix Hairpins
Small ribosomal subunit protein mS29 Chain: g
Molecule details ›
Chain: g
Length: 351 amino acids
Theoretical weight: 40.51 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: A6QQP1 (Residues: 74-424; Coverage: 83%)
Gene name: DAP3
Sequence domains: Mitochondrial ribosomal death-associated protein 3
Small ribosomal subunit protein mS31 Chain: h
Molecule details ›
Chain: h
Length: 386 amino acids
Theoretical weight: 43.74 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82925 (Residues: 1-386; 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: 12.48 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82926 (Residues: 1-106; Coverage: 100%)
Gene name: MRPS33
Sequence domains: Mitochondrial ribosomal subunit S27
Small ribosomal subunit protein mS35 Chain: k
Molecule details ›
Chain: k
Length: 325 amino acids
Theoretical weight: 37.13 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2YDF6 (Residues: 1-325; Coverage: 100%)
Gene names: MRPS28, MRPS35
Sequence domains: Mitochondrial ribosomal subunit protein
CHCH domain-containing protein Chain: m
Molecule details ›
Chain: m
Length: 118 amino acids
Theoretical weight: 13.58 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2HJE8 (Residues: 1-118; Coverage: 100%)
Gene name: CHCHD1
Sequence domains: CHCH domain
Small ribosomal subunit protein mS39 Chain: o
Molecule details ›
Chain: o
Length: 575 amino acids
Theoretical weight: 60.59 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2KI62 (Residues: 1-688; Coverage: 84%)
Gene names: MRPS39, PTCD3
Sequence domains: Pentatricopeptide repeat domain
Small ribosomal subunit protein uS2m Chain: B
Molecule details ›
Chain: B
Length: 293 amino acids
Theoretical weight: 31.78 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82923 (Residues: 1-293; Coverage: 100%)
Gene name: MRPS2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein bS6m Chain: F
Molecule details ›
Chain: F
Length: 124 amino acids
Theoretical weight: 14.17 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82931 (Residues: 1-124; Coverage: 100%)
Gene names: MRPS6, RPMS6
Sequence domains: Ribosomal protein S6
Structure domains: Alpha-Beta Plaits
Small ribosomal subunit protein uS11m Chain: K
Molecule details ›
Chain: K
Length: 197 amino acids
Theoretical weight: 20.87 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82911 (Residues: 1-197; Coverage: 100%)
Gene name: MRPS11
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Small ribosomal subunit protein uS15m Chain: O
Molecule details ›
Chain: O
Length: 256 amino acids
Theoretical weight: 29.25 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82913 (Residues: 1-256; Coverage: 100%)
Gene names: MRPS15, RPMS15
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS18m Chain: R
Molecule details ›
Chain: R
Length: 143 amino acids
Theoretical weight: 16.24 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82917 (Residues: 1-143; Coverage: 100%)
Gene name: MRPS18C
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS21m Chain: U
Molecule details ›
Chain: U
Length: 87 amino acids
Theoretical weight: 10.7 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82920 (Residues: 1-87; Coverage: 100%)
Gene names: MRPS21, RPMS21
Sequence domains: Ribosomal protein S21
Small ribosomal subunit protein mS23 Chain: b
Molecule details ›
Chain: b
Length: 190 amino acids
Theoretical weight: 21.63 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2NL27 (Residues: 1-190; Coverage: 100%)
Gene name: MRPS23
Sequence domains: Mitochondrial ribosomal protein S23
Small ribosomal subunit protein bS1m Chain: f
Molecule details ›
Chain: f
Length: 189 amino acids
Theoretical weight: 21.08 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P82928 (Residues: 1-189; Coverage: 100%)
Gene name: MRPS28
Sequence domains: Mitochondrial ribosomal protein MRP-S35
Small ribosomal subunit protein mS38 Chain: n
Molecule details ›
Chain: n
Length: 199 amino acids
Theoretical weight: 22.97 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q0VCJ1 (Residues: 1-199; Coverage: 100%)
Gene name: AURKAIP1
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Translation initiation factor IF-3, mitochondrial Chain: z
Molecule details ›
Chain: z
Length: 247 amino acids
Theoretical weight: 28.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H2K0 (Residues: 32-278; Coverage: 89%)
Gene names: DC38, MTIF3
Sequence domains: Translation initiation factor IF-3, N-terminal domain
28S ribosomal RNA, mitochondria Chain: A
Molecule details ›
Chain: A
Length: 955 nucleotides
Theoretical weight: 306.93 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.48Å
Relevant EMDB volumes: EMD-9362

Quick links

Citations

9 review citations

The Diseased Mitoribosome.
Ferrari et al. (2021)
8 more

1 mention without citation

Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors.
Nadler et al. (2022)