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Cryo-EM structure of yeast Ribonuclease P

Electron Microscopy
3.48Å resolution
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
Assembly composition:
hetero undecamer (preferred)
Entry contents: 9 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero undecamer
Accessible surface area: 160012.35 Å2
Buried surface area: 61194.71 Å2
Dissociation area: 2,280.23 Å2
Dissociation energy (ΔGdiss): 24.34 kcal/mol
Dissociation entropy (TΔSdiss): 13.37 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-250234

Macromolecules

Ribonucleases P/MRP protein subunit POP1
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
Pfam:
InterPro:
Ribonucleases P/MRP protein subunit POP1 in PDB entry 6agb, assembly 1, front view.
Ribonucleases P/MRP protein subunit POP1 in PDB entry 6agb, assembly 1, side view.
Ribonucleases P/MRP protein subunit POP1 in PDB entry 6agb, assembly 1, top view.
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Ribonucleases P/MRP protein subunit POP3
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
Pfam: RNase P subunit Pop3
InterPro: RNase P, subunit Pop3
Ribonucleases P/MRP protein subunit POP3 in PDB entry 6agb, assembly 1, front view.
Ribonucleases P/MRP protein subunit POP3 in PDB entry 6agb, assembly 1, side view.
Ribonucleases P/MRP protein subunit POP3 in PDB entry 6agb, assembly 1, top view.
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RNases MRP/P 32.9 kDa subunit
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
Pfam: Ribonuclease P/MRP, subunit p29
InterPro:
RNases MRP/P 32.9 kDa subunit in PDB entry 6agb, assembly 1, front view.
RNases MRP/P 32.9 kDa subunit in PDB entry 6agb, assembly 1, side view.
RNases MRP/P 32.9 kDa subunit in PDB entry 6agb, assembly 1, top view.
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Ribonuclease P/MRP protein subunit POP5
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
Pfam: Rpp14/Pop5 family
InterPro:
Ribonuclease P/MRP protein subunit POP5 in PDB entry 6agb, assembly 1, front view.
Ribonuclease P/MRP protein subunit POP5 in PDB entry 6agb, assembly 1, side view.
Ribonuclease P/MRP protein subunit POP5 in PDB entry 6agb, assembly 1, top view.
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Ribonucleases P/MRP protein subunit POP6
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
Pfam: Alba
InterPro: DNA/RNA-binding protein Alba-like
Ribonucleases P/MRP protein subunit POP6 in PDB entry 6agb, assembly 1, front view.
Ribonucleases P/MRP protein subunit POP6 in PDB entry 6agb, assembly 1, side view.
Ribonucleases P/MRP protein subunit POP6 in PDB entry 6agb, assembly 1, top view.
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Ribonucleases P/MRP protein subunit POP7
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
Pfam: Rpp20 subunit of nuclear RNase MRP and P
InterPro:
CATH: Alba-like domain
Ribonucleases P/MRP protein subunit POP7 in PDB entry 6agb, assembly 1, front view.
Ribonucleases P/MRP protein subunit POP7 in PDB entry 6agb, assembly 1, side view.
Ribonucleases P/MRP protein subunit POP7 in PDB entry 6agb, assembly 1, top view.
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Ribonucleases P/MRP protein subunit POP8
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
Pfam: Ribonucleases P/MRP protein subunit Pop8
InterPro: Ribonucleases P/MRP protein subunit Pop8
Ribonucleases P/MRP protein subunit POP8 in PDB entry 6agb, assembly 1, front view.
Ribonucleases P/MRP protein subunit POP8 in PDB entry 6agb, assembly 1, side view.
Ribonucleases P/MRP protein subunit POP8 in PDB entry 6agb, assembly 1, top view.
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Ribonuclease P/MRP protein subunit RPP1
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
Pfam: RNase P subunit p30
InterPro:
Ribonuclease P/MRP protein subunit RPP1 in PDB entry 6agb, assembly 1, front view.
Ribonuclease P/MRP protein subunit RPP1 in PDB entry 6agb, assembly 1, side view.
Ribonuclease P/MRP protein subunit RPP1 in PDB entry 6agb, assembly 1, top view.
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Ribonuclease P protein subunit RPR2
Chain: K
Length: 144 amino acids
Theoretical weight: 16.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40571 (Residues: 1-144; Coverage: 100%)
Gene names: RPR2, YIR015W
Pfam: RNAse P Rpr2/Rpp21/SNM1 subunit domain
InterPro: Ribonuclease P subunit, Rpr2/Snm1/Rpp21
Ribonuclease P protein subunit RPR2 in PDB entry 6agb, assembly 1, front view.
Ribonuclease P protein subunit RPR2 in PDB entry 6agb, assembly 1, side view.
Ribonuclease P protein subunit RPR2 in PDB entry 6agb, assembly 1, top view.
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RNA chain A
Name: Ribonuclease P RNA
Representative chains: A
Length: 369 nucleotides
Theoretical weight: 118.86 KDa
Rfam: Nuclear RNase P
Ribonuclease P RNA in PDB entry 6agb, assembly 1, front view.
Ribonuclease P RNA in PDB entry 6agb, assembly 1, side view.
Ribonuclease P RNA in PDB entry 6agb, assembly 1, top view.
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