6CWX

Crystal structure of human ribonuclease P/MRP proteins Rpp20/Rpp25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Human Rpp20/Rpp25 Reveals Quaternary Level Adaptation of the Alba Scaffold as Structural Basis for Single-stranded RNA Binding.

Chan, C.W.Kiesel, B.R.Mondragon, A.

(2018) J Mol Biol 430: 1403-1416

  • DOI: 10.1016/j.jmb.2018.03.029
  • Primary Citation of Related Structures:  
    6CWX

  • PubMed Abstract: 
  • Ribonuclease P (RNase P) catalyzes the removal of 5' leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share several of the same protein subunits, contain a similar catalytic RNA core, and exhibit structural features that do not exist in their bacterial or archaeal counterparts ...

    Ribonuclease P (RNase P) catalyzes the removal of 5' leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share several of the same protein subunits, contain a similar catalytic RNA core, and exhibit structural features that do not exist in their bacterial or archaeal counterparts. A unique feature of eukaryotic RNase P/MRP is the presence of two relatively long and unpaired internal loops within the P3 region of their RNA subunit bound by a heterodimeric protein complex, Rpp20/Rpp25. Here we present a crystal structure of the human Rpp20/Rpp25 heterodimer and we propose, using comparative structural analyses, that the evolutionary divergence of the single-stranded and helical nucleic acid binding specificities of eukaryotic Rpp20/Rpp25 and their related archaeal Alba chromatin protein dimers, respectively, originate primarily from quaternary level differences observed in their heterodimerization interface. Our work provides structural insights into how the archaeal Alba protein scaffold was adapted evolutionarily for incorporation into several functionally-independent eukaryotic ribonucleoprotein complexes.


    Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, United States. Electronic address: a-mondragon@northwestern.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p20A142Homo sapiensMutation(s): 0 
Gene Names: POP7RPP20
EC: 3.1.26.5
UniProt & NIH Common Fund Data Resources
Find proteins for O75817 (Homo sapiens)
Explore O75817 
Go to UniProtKB:  O75817
PHAROS:  O75817
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p25B201Homo sapiensMutation(s): 0 
Gene Names: RPP25
EC: 3.1.26.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUL9 (Homo sapiens)
Explore Q9BUL9 
Go to UniProtKB:  Q9BUL9
PHAROS:  Q9BUL9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B], F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.19α = 90
b = 182.19β = 90
c = 182.19γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
autoSHARPphasing
BUCCANEERmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM058443
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States4T32 GM008152
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32 GM008382

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence