› 6ahr

Electron Microscopy
3.92Å resolution

Cryo-EM structure of human Ribonuclease P

Released:
DOI: 10.2210/pdb6ahr/pdb
PDB entry 6ahr coloured by chain, front view.
PDB entry 6ahr coloured by chain, side view.
PDB entry 6ahr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cryo-EM Structure of the Human Ribonuclease P Holoenzyme.
Wu J, Niu S, Tan M, Huang C, Li M, Song Y, Wang Q, Chen J, Shi S, Lan P, Lei M
Cell 175 1393-1404.e11 (2018)
PMID: 30454648
Related structures: EMD-9626

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131127 (preferred)
Entry contents:
10 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (11 distinct):
Ribonucleases P/MRP protein subunit POP1 Chain: B
Molecule details ›
Chain: B
Length: 1024 amino acids
Theoretical weight: 114.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99575 (Residues: 1-1024; Coverage: 100%)
Gene names: KIAA0061, POP1
Sequence domains:
Ribonuclease P protein subunit p38 Chain: C
Molecule details ›
Chain: C
Length: 283 amino acids
Theoretical weight: 31.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P78345 (Residues: 1-283; Coverage: 100%)
Gene name: RPP38
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribonuclease P protein subunit p29 Chain: D
Molecule details ›
Chain: D
Length: 220 amino acids
Theoretical weight: 25.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95707 (Residues: 1-220; Coverage: 100%)
Gene names: POP4, RPP29
Sequence domains: Ribonuclease P/MRP, subunit p29
Ribonuclease P/MRP protein subunit POP5 Chain: E
Molecule details ›
Chain: E
Length: 163 amino acids
Theoretical weight: 18.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q969H6 (Residues: 1-163; Coverage: 100%)
Gene names: AD-008, HSPC004, POP5, x0003
Sequence domains: Rpp14/Pop5 family
Ribonuclease P protein subunit p25 Chain: F
Molecule details ›
Chain: F
Length: 199 amino acids
Theoretical weight: 20.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BUL9 (Residues: 1-199; Coverage: 100%)
Gene name: RPP25
Sequence domains: Alba
Ribonuclease P protein subunit p20 Chain: G
Molecule details ›
Chain: G
Length: 140 amino acids
Theoretical weight: 15.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75817 (Residues: 1-140; Coverage: 100%)
Gene names: POP7, RPP20
Sequence domains: Rpp20 subunit of nuclear RNase MRP and P
Ribonuclease P protein subunit p14 Chain: H
Molecule details ›
Chain: H
Length: 124 amino acids
Theoretical weight: 13.71 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95059 (Residues: 1-124; Coverage: 100%)
Gene name: RPP14
Sequence domains: Rpp14/Pop5 family
Ribonuclease P protein subunit p30 Chains: I, J
Molecule details ›
Chains: I, J
Length: 268 amino acids
Theoretical weight: 29.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P78346 (Residues: 1-268; Coverage: 100%)
Gene names: RNASEP2, RPP30
Sequence domains: RNase P subunit p30
Ribonuclease P protein subunit p21 Chain: K
Molecule details ›
Chain: K
Length: 154 amino acids
Theoretical weight: 17.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9H633 (Residues: 1-154; Coverage: 100%)
Gene names: C6orf135, CAT60, RPP21
Sequence domains: RNAse P Rpr2/Rpp21/SNM1 subunit domain
Ribonuclease P protein subunit p40 Chain: L
Molecule details ›
Chain: L
Length: 363 amino acids
Theoretical weight: 41.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75818 (Residues: 1-363; Coverage: 100%)
Gene names: RNASEP1, RPP40
Sequence domains: Ribonuclease P 40kDa (Rpp40) subunit
H1 RNA Chain: A
Molecule details ›
Chain: A
Length: 341 nucleotides
Theoretical weight: 110.24 KDa
Sequence domains: Nuclear RNase P

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.92Å
Relevant EMDB volumes: EMD-9626

Quick links

Citations

13 review citations

The many faces of RNA-based RNase P, an RNA-world relic.
Phan et al. (2021)
12 more

5 mentions without citation

The Dynamic Network of RNP RNase P Subunits.
Shaukat et al. (2021)
4 more