1BC4

THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTES OF RANA CATESBEIANA (BULLFROG), NMR, 15 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 15 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The solution structure of a cytotoxic ribonuclease from the oocytes of Rana catesbeiana (bullfrog).

Chang, C.F.Chen, C.Chen, Y.C.Hom, K.Huang, R.F.Huang, T.H.

(1998) J Mol Biol 283: 231-244

  • DOI: 10.1006/jmbi.1998.2082
  • Primary Citation of Related Structures:  
    1BC4

  • PubMed Abstract: 
  • RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a lectin possessing potent cell cytotoxicity. It was isolated from the oocytes of Rana catesbeiana (bull frog). From analysis of an extensive set of 1H homonuclear 2D NMR spectra we have completed the resonance assignments ...

    RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a lectin possessing potent cell cytotoxicity. It was isolated from the oocytes of Rana catesbeiana (bull frog). From analysis of an extensive set of 1H homonuclear 2D NMR spectra we have completed the resonance assignments. Determination of the three-dimensional structure was carried out with the program X-PLOR using a total of 951 restraints including 814 NMR-derived distances, 61 torsion angles, and 76 hydrogen bond restraints. In the resultant family of 15 best structures, selected from a total of 150 calculated structures, the root-mean-square deviation from the average structure for the backbone heavy-atoms involved in well-defined secondary structure is 0.48 A, while that for all backbone heavy-atoms is 0.91 A. The structure of RC-RNase consists of three alpha-helices and two triple-stranded anti-parallel beta-sheets and folds in a kidney-shape, very similar to the X-ray crystal structure of a homolo gous protein, onconase isolated from Rana pipiens. We have also investigated the interaction between RC-RNase and two inhibitors, cytidylyl(2'-->5')guanosine (2',5'-CpG) and 2'-deoxycytidylyl(3'-->5')-2'-deoxyguanosine (3',5'-dCpdG). Based on the ligand-induced chemical shift changes in RC-RNase and the NOE cross-peaks between RC-RNase and the inhibitors, the key residues involved in protein-inhibitor interaction have been identified. The inhibitors were found to bind in a "retro-binding" mode, with the guanine base bonded to the B1 subsite. The His103 residue was found to occupy the B state with the imidazole ring pointing away from the active site. The structure coordinates and the NMR restraints have been deposited in the Brookhaven Protein Data Bank (1bc4 and 1bc4mr, respectively).


    Related Citations: 
    • The Secondary Structure of a Pyrimidine-Guanine Sequence-Specific Ribonuclease Possessing Cytotoxic Activity from the Oocytes of Rana Catesbeiana
      Chen, C., Hom, K., Huang, R.F., Chou, P.J., Liao, Y.D., Huang, T.
      (1996) J Biomol NMR 8: 331

    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan, 11529, The Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASEA111Lithobates catesbeianusMutation(s): 0 
Gene Names: RCR
EC: 3.1.27.5 (PDB Primary Data), 3.1.27 (UniProt)
UniProt
Find proteins for P11916 (Lithobates catesbeianus)
Explore P11916 
Go to UniProtKB:  P11916
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11916
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 15 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Other, Polymer sequence