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› 6agb

Electron Microscopy
3.48Å resolution

Cryo-EM structure of yeast Ribonuclease P

Released:
DOI: 10.2210/pdb6agb/pdb
PDB entry 6agb coloured by chain, front view.
PDB entry 6agb coloured by chain, side view.
PDB entry 6agb coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural insight into precursor tRNA processing by yeast ribonuclease P.
Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M
Science 362 (2018)
PMID: 30262633
Related structures: EMD-9616

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-302750 (preferred)
Entry contents:
9 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (10 distinct):
Ribonucleases P/MRP protein subunit POP1 Chain: B
Molecule details ›
Chain: B
Length: 875 amino acids
Theoretical weight: 100.56 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P41812 (Residues: 1-875; Coverage: 100%)
Gene names: N1285, POP1, YNL221C
Sequence domains:
Ribonucleases P/MRP protein subunit POP3 Chain: C
Molecule details ›
Chain: C
Length: 195 amino acids
Theoretical weight: 22.64 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53833 (Residues: 1-195; Coverage: 100%)
Gene names: N0586, POP3, YNL282W
Sequence domains: RNase P subunit Pop3
RNases MRP/P 32.9 kDa subunit Chain: D
Ribonuclease P/MRP protein subunit POP5 Chain: E
Ribonucleases P/MRP protein subunit POP6 Chain: F
Ribonucleases P/MRP protein subunit POP7 Chain: G
Ribonucleases P/MRP protein subunit POP8 Chain: H
Ribonuclease P/MRP protein subunit RPP1 Chains: I, J
Ribonuclease P protein subunit RPR2 Chain: K
Ribonuclease P RNA Chain: A

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.48Å
Relevant EMDB volumes: EMD-9616

Quick links

Citations

9 review citations

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

1 mention without citation

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