3IAB

Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3 domain of RNase MRP RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

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This is version 1.1 of the entry. See complete history


Literature

Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain

Perederina, A.Esakova, O.Quan, C.Khanova, E.Krasilnikov, A.S.

(2010) EMBO J 29: 761-769

  • DOI: https://doi.org/10.1038/emboj.2009.396
  • Primary Citation of Related Structures:  
    3IAB

  • PubMed Abstract: 

    Ribonuclease (RNase) P is a site-specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a catalytic RNA component and a protein moiety. In the eukaryotes, the RNase P lineage has split into two, giving rise to a closely related enzyme, RNase MRP, which has similar components but has evolved to have different specificities. The eukaryotic RNases P/MRP have acquired an essential helix-loop-helix protein-binding RNA domain P3 that has an important function in eukaryotic enzymes and distinguishes them from bacterial and archaeal RNases P. Here, we present a crystal structure of the P3 RNA domain from Saccharomyces cerevisiae RNase MRP in a complex with RNase P/MRP proteins Pop6 and Pop7 solved to 2.7 A. The structure suggests similar structural organization of the P3 RNA domains in RNases P/MRP and possible functions of the P3 domains and proteins bound to them in the stabilization of the holoenzymes' structures as well as in interactions with substrates. It provides the first insight into the structural organization of the eukaryotic enzymes of the RNase P/MRP family.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleases P/MRP protein subunit POP6158Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POP6YGR030C
EC: 3.1.26.5
UniProt
Find proteins for P53218 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53218 
Go to UniProtKB:  P53218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53218
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleases P/MRP protein subunit POP7140Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POP7RPP2YBR1219YBR167C
EC: 3.1.26.5
UniProt
Find proteins for P38291 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38291 
Go to UniProtKB:  P38291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38291
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
P3 domain of the RNA component of RNase MRPC [auth R]46N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.514α = 90
b = 126.514β = 90
c = 76.766γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance