1DZA

3-D structure of a HP-RNase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-Dimensional Structure of a Human Pancreatic Ribonuclease Variant, a Step Forward in the Design of Cytotoxic Ribonucleases

Pous, J.Canals, A.Terzyan, S.S.Guasch, A.Benito, A.Ribo, M.Vilanova, M.Coll, M.

(2000) J Mol Biol 303: 49

  • DOI: https://doi.org/10.1006/jmbi.2000.4506
  • Primary Citation of Related Structures:  
    1DZA

  • PubMed Abstract: 

    We have determined the crystal structure of a human pancreatic ribonuclease or RNase 1 variant at 1.65 A resolution. Five residues in the N-terminal region were substituted by the corresponding amino acids of the bovine seminal RNase. In addition, a Pro to Ser mutation was present at position 50. The substitution of part of the N terminus has been critical both in improving the expression of this enzyme as a recombinant protein and in achieving its crystallisation. The determination of the crystal structure revealed the characteristic RNase fold including a V-shaped beta-sheet and three alpha-helices. It differs from its bovine RNase orthologue mainly in the loop regions. The active-site cleft shows a similar architecture to that of its bovine counterpart, with the essential residues occupying equivalent positions. In the present structure, however, His119 is displaced as it is in the structure of RNase A at high pH. An interaction model of human ribonuclease with the ribonuclease inhibitor, together with inhibition assays, indicate that, in contrast to RNase A, the modification of the loop beta4beta5 is not enough to avoid inhibition. This study represents the first crystallographic approach to the human enzyme, and should constitute an invaluable tool for the design of ribonuclease variants with acquired cytotoxic properties.


  • Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, CID-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RIBONUCLEASE 1
A, B
129Homo sapiensMutation(s): 7 
Gene Names: PM7
EC: 3.1.27.5
UniProt & NIH Common Fund Data Resources
Find proteins for P07998 (Homo sapiens)
Explore P07998 
Go to UniProtKB:  P07998
PHAROS:  P07998
GTEx:  ENSG00000129538 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07998
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, B
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.85α = 90
b = 67.42β = 90
c = 114.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-16
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2023-12-06
    Changes: Advisory, Data collection, Database references, Refinement description