3TSR

X-ray structure of mouse ribonuclease inhibitor complexed with mouse ribonuclease 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1999 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Functional evolution of ribonuclease inhibitor: insights from birds and reptiles.

Lomax, J.E.Bianchetti, C.M.Chang, A.Phillips, G.N.Fox, B.G.Raines, R.T.

(2014) J.Mol.Biol. 426: 3041-3056

  • DOI: 10.1016/j.jmb.2014.06.007
  • Primary Citation of Related Structures:  4PEQ, 4PER

  • PubMed Abstract: 
  • Ribonuclease inhibitor (RI) is a conserved protein of the mammalian cytosol. RI binds with high affinity to diverse secretory ribonucleases (RNases) and inhibits their enzymatic activity. Although secretory RNases are found in all vertebrates, the ex ...

    Ribonuclease inhibitor (RI) is a conserved protein of the mammalian cytosol. RI binds with high affinity to diverse secretory ribonucleases (RNases) and inhibits their enzymatic activity. Although secretory RNases are found in all vertebrates, the existence of a non-mammalian RI has been uncertain. Here, we report on the identification and characterization of RI homologs from chicken and anole lizard. These proteins bind to RNases from multiple species but exhibit much greater affinity for their cognate RNases than for mammalian RNases. To reveal the basis for this differential affinity, we determined the crystal structure of mouse, bovine, and chicken RI·RNase complexes to a resolution of 2.20, 2.21, and 1.92Å, respectively. A combination of structural, computational, and bioinformatic analyses enabled the identification of two residues that appear to contribute to the differential affinity for RNases. We also found marked differences in oxidative instability between mammalian and non-mammalian RIs, indicating evolution toward greater oxygen sensitivity in RIs from mammalian species. Taken together, our results illuminate the structural and functional evolution of RI, along with its dynamic role in vertebrate biology.


    Organizational Affiliation

    Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B, C, D
125Mus musculusGene Names: Rnase1 (Rib-1, Rib1, Rns1)
EC: 3.1.27.5
Find proteins for P00683 (Mus musculus)
Go to UniProtKB:  P00683
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease inhibitor
E, F, G, H
457Mus musculusGene Names: Rnh1 (Rnh)
Find proteins for Q91VI7 (Mus musculus)
Go to UniProtKB:  Q91VI7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, E, F, G, H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
E
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1999 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.396α = 90.00
b = 125.341β = 94.72
c = 123.064γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2014-06-18
    Type: Database references
  • Version 1.2: 2014-07-02
    Type: Database references
  • Version 1.3: 2014-08-20
    Type: Database references
  • Version 1.4: 2017-11-08
    Type: Refinement description