› 7pny

Electron Microscopy
3.06Å resolution

Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation b

Released:
DOI: 10.2210/pdb7pny/pdb
PDB entry 7pny coloured by chain, front view.
PDB entry 7pny coloured by chain, side view.
PDB entry 7pny coloured by chain, top view.
Source organism: Homo sapiens
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-13556

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-249540 (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: 296 amino acids
Theoretical weight: 33.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y399 (Residues: 1-296; Coverage: 100%)
Gene names: CGI-91, MRPS2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3m Chain: C
Molecule details ›
Chain: C
Length: 167 amino acids
Theoretical weight: 19.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EL2 (Residues: 1-167; Coverage: 100%)
Gene names: HSPC335, MRPS24
Sequence domains: Mitochondrial ribosome subunit S24
Small ribosomal subunit protein uS5m Chain: D
Molecule details ›
Chain: D
Length: 430 amino acids
Theoretical weight: 48.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82675 (Residues: 1-430; Coverage: 100%)
Gene name: MRPS5
Sequence domains:
Small ribosomal subunit protein bS6m Chain: E
Molecule details ›
Chain: E
Length: 125 amino acids
Theoretical weight: 14.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82932 (Residues: 1-125; Coverage: 100%)
Gene names: C21orf101, MRPS6, RPMS6
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7m Chain: F
Molecule details ›
Chain: F
Length: 242 amino acids
Theoretical weight: 28.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2R9 (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: 396 amino acids
Theoretical weight: 45.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82933 (Residues: 1-396; Coverage: 100%)
Gene names: MRPS9, RPMS9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10m Chain: H
Molecule details ›
Chain: H
Length: 201 amino acids
Theoretical weight: 23.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82664 (Residues: 1-201; Coverage: 100%)
Gene names: MRPS10, MSTP040
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11m Chain: I
Molecule details ›
Chain: I
Length: 194 amino acids
Theoretical weight: 20.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82912 (Residues: 1-194; Coverage: 100%)
Gene names: HCC2, MRPS11, RPMS11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12m Chain: J
Molecule details ›
Chain: J
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15235 (Residues: 1-138; Coverage: 100%)
Gene names: MRPS12, RPMS12, RPSM12
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS14m Chain: K
Molecule details ›
Chain: K
Length: 128 amino acids
Theoretical weight: 15.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60783 (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: 257 amino acids
Theoretical weight: 29.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82914 (Residues: 1-257; Coverage: 100%)
Gene names: DC37, MRPS15, RPMS15
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16m Chain: M
Molecule details ›
Chain: M
Length: 137 amino acids
Theoretical weight: 15.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3D3 (Residues: 1-137; Coverage: 100%)
Gene names: CGI-132, MRPS16, RPMS16
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17m Chain: N
Molecule details ›
Chain: N
Length: 130 amino acids
Theoretical weight: 14.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2R5 (Residues: 1-130; Coverage: 100%)
Gene names: HSPC011, MRPS17, RPMS17
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein mS40 Chain: O
Molecule details ›
Chain: O
Length: 258 amino acids
Theoretical weight: 29.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y676 (Residues: 1-258; Coverage: 100%)
Gene names: C6orf14, HSPC183, MRPS18B, PTD017
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS18m Chain: P
Molecule details ›
Chain: P
Length: 142 amino acids
Theoretical weight: 15.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3D5 (Residues: 1-142; Coverage: 100%)
Gene names: CGI-134, MRPS18C
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS21m Chain: Q
Molecule details ›
Chain: Q
Length: 86 amino acids
Theoretical weight: 10.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82921 (Residues: 2-87; Coverage: 99%)
Gene names: MDS016, MRPS21, RPMS21
Sequence domains: Ribosomal protein S21
Small ribosomal subunit protein mS22 Chain: R
Molecule details ›
Chain: R
Length: 360 amino acids
Theoretical weight: 41.34 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82650 (Residues: 1-360; Coverage: 100%)
Gene names: C3orf5, GK002, MRPS22, RPMS22
Sequence domains: Mitochondrial 28S ribosomal protein S22
Small ribosomal subunit protein mS23 Chain: S
Molecule details ›
Chain: S
Length: 190 amino acids
Theoretical weight: 21.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3D9 (Residues: 1-190; Coverage: 100%)
Gene names: CGI-138, HSPC329, MRPS23
Sequence domains: Mitochondrial ribosomal protein S23
Small ribosomal subunit protein mS25 Chain: T
Molecule details ›
Chain: T
Length: 173 amino acids
Theoretical weight: 20.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82663 (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: U
Molecule details ›
Chain: U
Length: 205 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYN8 (Residues: 1-205; Coverage: 100%)
Gene names: C20orf193, MRPS26, RPMS13
Sequence domains: Mitochondrial ribosome subunit S26
Small ribosomal subunit protein mS27 Chain: V
Molecule details ›
Chain: V
Length: 414 amino acids
Theoretical weight: 47.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92552 (Residues: 1-414; Coverage: 100%)
Gene names: KIAA0264, MRPS27
Sequence domains: Mitochondrial 28S ribosomal protein S27
Small ribosomal subunit protein bS1m Chain: W
Molecule details ›
Chain: W
Length: 187 amino acids
Theoretical weight: 20.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2Q9 (Residues: 1-187; Coverage: 100%)
Gene names: HSPC007, MRPS28, MRPS35
Sequence domains: Mitochondrial ribosomal protein MRP-S35
Small ribosomal subunit protein mS29 Chain: X
Molecule details ›
Chain: X
Length: 398 amino acids
Theoretical weight: 45.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P51398 (Residues: 1-398; 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: 395 amino acids
Theoretical weight: 45.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92665 (Residues: 1-395; 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: 12.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y291 (Residues: 1-106; Coverage: 100%)
Gene names: CGI-139, MRPS33, PTD003
Sequence domains: Mitochondrial ribosomal subunit S27
Small ribosomal subunit protein mS34 Chain: 0
Molecule details ›
Chain: 0
Length: 218 amino acids
Theoretical weight: 25.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82930 (Residues: 1-218; Coverage: 100%)
Gene name: MRPS34
Sequence domains: Mitochondrial 28S ribosomal protein S34
Small ribosomal subunit protein mS35 Chain: 1
Molecule details ›
Chain: 1
Length: 323 amino acids
Theoretical weight: 36.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82673 (Residues: 1-323; Coverage: 100%)
Gene names: HDCMD11P, MDS023, MRPS28, MRPS35, PSEC0213
Sequence domains: Mitochondrial ribosomal subunit protein
Small ribosomal subunit protein mS38 Chain: 3
Molecule details ›
Chain: 3
Length: 199 amino acids
Theoretical weight: 22.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NWT8 (Residues: 1-199; 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: 689 amino acids
Theoretical weight: 78.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EY7 (Residues: 1-689; Coverage: 100%)
Gene names: MRPS39, PTCD3, TRG15
Sequence domains:
Putative ribosome-binding factor A, mitochondrial Chain: a
Molecule details ›
Chain: a
Length: 343 amino acids
Theoretical weight: 38.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N0V3 (Residues: 1-343; Coverage: 100%)
Gene names: C18orf22, RBFA
Sequence domains: Ribosome-binding factor A
12S rRNA N(4)-cytidine methyltransferase METTL15 Chain: b
Molecule details ›
Chain: b
Length: 407 amino acids
Theoretical weight: 46.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: A6NJ78 (Residues: 1-407; Coverage: 100%)
Gene names: METT5D1, METTL15
Sequence domains: MraW methylase family
12S mitochondrial rRNA Chain: A
Molecule details ›
Chain: A
Length: 955 nucleotides
Theoretical weight: 306.55 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

8 bound ligands:
Ligand NAD 1 x NAD
Ligand MG 61 x MG
Ligand K 20 x K
Ligand ZN 1 x ZN
Ligand FES 2 x FES
Ligand ATP 1 x ATP
Ligand GDP 1 x GDP
Ligand SAH 1 x SAH
5 modified residues:
Ligand 5MU 1 x 5MU
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-13556

Quick links

Citations

2 review citations

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

1 mention without citation

Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15.
Lv et al. (2024)