2BNH

PORCINE RIBONUCLEASE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A.

Kobe, B.Deisenhofer, J.

(1996) J.Mol.Biol. 264: 1028-1043

  • DOI: 10.1006/jmbi.1996.0694

  • PubMed Abstract: 
  • We describe the mechanism of ribonuclease inhibition by ribonuclease inhibitor, a protein built of leucine-rich repeats, based on the crystal structure of the complex between the inhibitor and ribonuclease A. The structure was determined by molecular ...

    We describe the mechanism of ribonuclease inhibition by ribonuclease inhibitor, a protein built of leucine-rich repeats, based on the crystal structure of the complex between the inhibitor and ribonuclease A. The structure was determined by molecular replacement and refined to an Rcryst of 19.4% at 2.5 A resolution. Ribonuclease A binds to the concave region of the inhibitor protein comprising its parallel beta-sheet and loops. The inhibitor covers the ribonuclease active site and directly contacts several active-site residues. The inhibitor only partially mimics the RNase-nucleotide interaction and does not utilize the p1 phosphate-binding pocket of ribonuclease A, where a sulfate ion remains bound. The 2550 A2 of accessible surface area buried upon complex formation may be one of the major contributors to the extremely tight association (Ki = 5.9 x 10(-14) M). The interaction is predominantly electrostatic; there is a high chemical complementarity with 18 putative hydrogen bonds and salt links, but the shape complementarity is lower than in most other protein-protein complexes. Ribonuclease inhibitor changes its conformation upon complex formation; the conformational change is unusual in that it is a plastic reorganization of the entire structure without any obvious hinge and reflects the conformational flexibility of the structure of the inhibitor. There is a good agreement between the crystal structure and other biochemical studies of the interaction. The structure suggests that the conformational flexibility of RI and an unusually large contact area that compensates for a lower degree of complementarity may be the principal reasons for the ability of RI to potently inhibit diverse ribonucleases. However, the inhibition is lost with amphibian ribonucleases that have substituted most residues corresponding to inhibitor-binding residues in RNase A, and with bovine seminal ribonuclease that prevents inhibitor binding by forming a dimer.


    Related Citations: 
    • Crystal Structure of Porcine Ribonuclease Inhibitor, a Protein with Leucine-Rich Repeats
      Kobe, B.,Deisenhofer, J.
      (1993) Nature 366: 751
    • Crystallization and Preliminary X-Ray Analysis of Porcine Ribonuclease Inhibitor, a Protein with Leucine-Rich Repeats
      Kobe, B.,Deisenhofer, J.
      (1993) J.Mol.Biol. 231: 137


    Organizational Affiliation

    St. Vincent's Institute of Medical Research, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE INHIBITOR
A
457Sus scrofaMutation(s): 0 
Gene Names: RNH1 (RI, RNH)
Find proteins for P10775 (Sus scrofa)
Go to Gene View: RNH1
Go to UniProtKB:  P10775
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.200 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 134.900α = 90.00
b = 134.900β = 90.00
c = 83.600γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
NIELSENdata reduction
X-PLORmodel building
X-PLORrefinement
XUONG)data reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance