› 7c79

Electron Microscopy
2.5Å resolution

Cryo-EM structure of yeast Ribonuclease MRP

Released:
DOI: 10.2210/pdb7c79/pdb
PDB entry 7c79 coloured by chain, front view.
PDB entry 7c79 coloured by chain, side view.
PDB entry 7c79 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural insight into precursor ribosomal RNA processing by ribonuclease MRP.
Lan P, Zhou B, Tan M, Li S, Cao M, Wu J, Lei M
Science 369 656-663 (2020)
PMID: 32586950
Related structures: EMD-30296

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-151147 (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: 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
Molecule details ›
Chain: D
Length: 279 amino acids
Theoretical weight: 32.93 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38336 (Residues: 1-279; Coverage: 100%)
Gene names: POP4, YBR1725, YBR257W
Sequence domains: Ribonuclease P/MRP, subunit p29
Ribonuclease P/MRP protein subunit POP5 Chain: E
Molecule details ›
Chain: E
Length: 173 amino acids
Theoretical weight: 19.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P28005 (Residues: 1-173; Coverage: 100%)
Gene names: FUN53, POP5, YAL033W
Sequence domains: Rpp14/Pop5 family
Ribonucleases P/MRP protein subunit POP6 Chain: F
Molecule details ›
Chain: F
Length: 158 amino acids
Theoretical weight: 18.23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53218 (Residues: 1-158; Coverage: 100%)
Gene names: POP6, YGR030C
Sequence domains: Alba
Ribonucleases P/MRP protein subunit POP7 Chain: G
Molecule details ›
Chain: G
Length: 140 amino acids
Theoretical weight: 15.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38291 (Residues: 1-140; Coverage: 100%)
Gene names: POP7, RPP2, YBR1219, YBR167C
Sequence domains: Rpp20 subunit of nuclear RNase MRP and P
Ribonucleases P/MRP protein subunit POP8 Chain: H
Molecule details ›
Chain: H
Length: 133 amino acids
Theoretical weight: 15.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38208 (Residues: 1-133; Coverage: 100%)
Gene names: POP8, YBL018C, YBL0301
Sequence domains: Ribonucleases P/MRP protein subunit Pop8
Ribonuclease P/MRP protein subunit RPP1 Chains: I, J
Molecule details ›
Chains: I, J
Length: 293 amino acids
Theoretical weight: 32.27 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38786 (Residues: 1-293; Coverage: 100%)
Gene names: RPP1, YHR062C
Sequence domains: RNase P subunit p30
Ribonuclease MRP protein subunit SNM1 Chain: K
Molecule details ›
Chain: K
Length: 198 amino acids
Theoretical weight: 22.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40993 (Residues: 1-198; Coverage: 100%)
Gene names: D8035.21, SNM1, YDR478W
Sequence domains: RNAse P Rpr2/Rpp21/SNM1 subunit domain
Ribonuclease MRP protein subunit RMP1 Chain: L
Molecule details ›
Chain: L
Length: 201 amino acids
Theoretical weight: 23.66 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12530 (Residues: 1-201; Coverage: 100%)
Gene names: RMP1, YLR145W
Sequence domains: Ribonuclease MRP protein subunit RMP1
Ribonuclease MRP RNA subunit NME1 Chain: A
Molecule details ›
Chain: A
Length: 340 nucleotides
Theoretical weight: 108.81 KDa
Sequence domains: RNase MRP

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.5Å
Relevant EMDB volumes: EMD-30296

Quick links

Citations

7 review citations

Long noncoding RNA and protein abundance in lncRNPs.
Wu et al. (2021)
6 more

1 mention without citation

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)