› 7pnv

Electron Microscopy
3.06Å resolution

Assembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA and Mettl15

Released:
DOI: 10.2210/pdb7pnv/pdb
PDB entry 7pnv coloured by chain, front view.
PDB entry 7pnv coloured by chain, side view.
PDB entry 7pnv coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
OpenAccess logo Nature 606 603-608 (2022)
PMID: 35676484
Related structures: EMD-13553

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-519775 (preferred)
Entry contents:
31 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (32 distinct):
Small ribosomal subunit protein uS2m Chain: B
Molecule details ›
Chain: B
Length: 291 amino acids
Theoretical weight: 32.36 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q924T2 (Residues: 1-291; Coverage: 100%)
Gene name: Mrps2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3m Chain: C
Molecule details ›
Chain: C
Length: 167 amino acids
Theoretical weight: 18.93 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQV5 (Residues: 1-167; Coverage: 100%)
Gene name: Mrps24
Sequence domains: Mitochondrial ribosome subunit S24
Small ribosomal subunit protein uS5m Chain: D
Molecule details ›
Chain: D
Length: 432 amino acids
Theoretical weight: 48.29 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q99N87 (Residues: 1-432; Coverage: 100%)
Gene name: Mrps5
Sequence domains:
Small ribosomal subunit protein bS6m Chain: E
Molecule details ›
Chain: E
Length: 125 amino acids
Theoretical weight: 14.33 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P58064 (Residues: 1-125; Coverage: 100%)
Gene names: Mrps6, Rpms6
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7m Chain: F
Molecule details ›
Chain: F
Length: 242 amino acids
Theoretical weight: 28.11 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q80X85 (Residues: 1-242; Coverage: 100%)
Gene name: Mrps7
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9m Chain: G
Molecule details ›
Chain: G
Length: 390 amino acids
Theoretical weight: 45 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D7N3 (Residues: 1-390; Coverage: 100%)
Gene name: Mrps9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10m Chain: H
Molecule details ›
Chain: H
Length: 160 amino acids
Theoretical weight: 18.73 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q80ZK0 (Residues: 1-160; Coverage: 100%)
Gene name: Mrps10
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11m Chain: I
Molecule details ›
Chain: I
Length: 191 amino acids
Theoretical weight: 20.25 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DCA2 (Residues: 1-191; Coverage: 100%)
Gene name: Mrps11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12m Chain: J
Molecule details ›
Chain: J
Length: 139 amino acids
Theoretical weight: 15.47 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: O35680 (Residues: 1-139; Coverage: 100%)
Gene names: Mrps12, Rpms12
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS14m Chain: K
Molecule details ›
Chain: K
Length: 128 amino acids
Theoretical weight: 14.95 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CR88 (Residues: 1-128; Coverage: 100%)
Gene name: Mrps14
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15m Chain: L
Molecule details ›
Chain: L
Length: 258 amino acids
Theoretical weight: 29.52 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DC71 (Residues: 1-258; Coverage: 100%)
Gene names: Mrps15, Rpms15
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16m Chain: M
Molecule details ›
Chain: M
Length: 135 amino acids
Theoretical weight: 15.22 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CPX7 (Residues: 1-135; Coverage: 100%)
Gene names: Mrps16, Rpms16
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17m Chain: N
Molecule details ›
Chain: N
Length: 120 amino acids
Theoretical weight: 13.41 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CQE3 (Residues: 1-120; Coverage: 100%)
Gene names: Mrps17, Rpms17
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein mS40 Chain: O
Molecule details ›
Chain: O
Length: 254 amino acids
Theoretical weight: 28.74 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q99N84 (Residues: 1-254; Coverage: 100%)
Gene name: Mrps18b
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS18m Chain: P
Molecule details ›
Chain: P
Length: 143 amino acids
Theoretical weight: 16.3 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8R2L5 (Residues: 1-143; Coverage: 100%)
Gene name: Mrps18c
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS21m Chain: Q
Molecule details ›
Chain: Q
Length: 86 amino acids
Theoretical weight: 10.49 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P58059 (Residues: 2-87; Coverage: 99%)
Gene names: Mrps21, Rpms21
Sequence domains: Ribosomal protein S21
Small ribosomal subunit protein mS22 Chain: R
Molecule details ›
Chain: R
Length: 359 amino acids
Theoretical weight: 41.26 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CXW2 (Residues: 1-359; Coverage: 100%)
Gene names: Mrps22, Rpms22
Sequence domains: Mitochondrial 28S ribosomal protein S22
Small ribosomal subunit protein mS23 Chain: S
Molecule details ›
Chain: S
Length: 177 amino acids
Theoretical weight: 20.38 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8VE22 (Residues: 1-177; Coverage: 100%)
Gene name: Mrps23
Sequence domains: Mitochondrial ribosomal protein S23
Small ribosomal subunit protein mS25 Chain: T
Molecule details ›
Chain: T
Length: 171 amino acids
Theoretical weight: 19.95 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D125 (Residues: 1-171; Coverage: 100%)
Gene names: Mrps25, Rpms25
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Small ribosomal subunit protein mS26 Chain: U
Molecule details ›
Chain: U
Length: 200 amino acids
Theoretical weight: 23.48 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q80ZS3 (Residues: 1-200; Coverage: 100%)
Gene name: Mrps26
Sequence domains: Mitochondrial ribosome subunit S26
Small ribosomal subunit protein mS27 Chain: V
Molecule details ›
Chain: V
Length: 415 amino acids
Theoretical weight: 47.84 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8BK72 (Residues: 1-415; Coverage: 100%)
Gene name: Mrps27
Sequence domains: Mitochondrial 28S ribosomal protein S27
Small ribosomal subunit protein bS1m Chain: W
Molecule details ›
Chain: W
Length: 186 amino acids
Theoretical weight: 20.56 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9CY16 (Residues: 1-186; Coverage: 100%)
Gene name: Mrps28
Sequence domains: Mitochondrial ribosomal protein MRP-S35
Small ribosomal subunit protein mS29 Chain: X
Molecule details ›
Chain: X
Length: 391 amino acids
Theoretical weight: 44.77 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9ER88 (Residues: 1-391; Coverage: 100%)
Gene names: Dap3, Mrps29
Sequence domains: Mitochondrial ribosomal death-associated protein 3
Small ribosomal subunit protein mS31 Chain: Y
Molecule details ›
Chain: Y
Length: 384 amino acids
Theoretical weight: 43.95 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q61733 (Residues: 1-384; Coverage: 100%)
Gene names: Imogn38, Mrps31
Sequence domains: Mitochondrial 28S ribosomal protein S31
Small ribosomal subunit protein mS33 Chain: Z
Molecule details ›
Chain: Z
Length: 106 amino acids
Theoretical weight: 12.49 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9D2R8 (Residues: 1-106; Coverage: 100%)
Gene names: Gdap3, Mrps33
Sequence domains: Mitochondrial ribosomal subunit S27
Small ribosomal subunit protein mS34 Chain: 0
Molecule details ›
Chain: 0
Length: 218 amino acids
Theoretical weight: 25.87 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9JIK9 (Residues: 1-218; Coverage: 100%)
Gene names: Mrps34, Tce2
Sequence domains: Mitochondrial 28S ribosomal protein S34
Small ribosomal subunit protein mS35 Chain: 1
Molecule details ›
Chain: 1
Length: 320 amino acids
Theoretical weight: 36.03 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q8BJZ4 (Residues: 1-320; Coverage: 100%)
Gene name: Mrps35
Sequence domains: Mitochondrial ribosomal subunit protein
Small ribosomal subunit protein mS38 Chain: 3
Molecule details ›
Chain: 3
Length: 200 amino acids
Theoretical weight: 23.35 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DCJ7 (Residues: 1-200; Coverage: 100%)
Gene names: Aip, Akip, Aurkaip1, Mrps38
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein mS39 Chain: 4
Molecule details ›
Chain: 4
Length: 685 amino acids
Theoretical weight: 77.89 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q14C51 (Residues: 1-685; Coverage: 100%)
Gene names: Mrps39, Ptcd3
Sequence domains:
Putative ribosome-binding factor A, mitochondrial Chain: a
Molecule details ›
Chain: a
Length: 350 amino acids
Theoretical weight: 39.38 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q6P3B9 (Residues: 1-350; Coverage: 100%)
Gene name: Rbfa
Sequence domains: Ribosome-binding factor A
12S rRNA N(4)-cytidine methyltransferase METTL15 Chain: b
Molecule details ›
Chain: b
Length: 406 amino acids
Theoretical weight: 45.34 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q9DCL4 (Residues: 1-406; Coverage: 100%)
Gene names: Mett5d1, Mettl15
Sequence domains: MraW methylase family
12S mitochondrial rRNA Chain: A
Molecule details ›
Chain: A
Length: 956 nucleotides
Theoretical weight: 306.88 KDa
Sequence domains: Microsporidia small subunit ribosomal RNA

Ligands and Environments

6 bound ligands:
Ligand MG 49 x MG
Ligand K 13 x K
Ligand ZN 1 x ZN
Ligand FES 2 x FES
Ligand ATP 1 x ATP
Ligand SAH 1 x SAH
4 modified residues:
Ligand B8T 1 x B8T
Ligand 5MC 1 x 5MC
Ligand MA6 2 x MA6
Ligand AYA 1 x AYA

Experiments and Validation Details

Entry percentile scores
Resolution: 3.06Å
Relevant EMDB volumes: EMD-13553

Quick links

Citations

2 review citations

GTPase Era at the heart of ribosome assembly.
Gruffaz et al. (2023)
1 more