1JVU

CRYSTAL STRUCTURE OF RIBONUCLEASE A (COMPLEXED FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Reversible Substrate-Induced Domain Motions in Ribonuclease A

Vitagliano, L.Merlino, A.Zagari, A.Mazzarella, L.

(2002) Proteins 46: 97-104

  • DOI: 10.1002/prot.10033
  • Primary Citation of Related Structures:  
    1JVT, 1JVV, 1JVU

  • PubMed Abstract: 
  • Despite the increasing number of successful determinations of complex protein structures the understanding of their dynamics properties is still rather limited. Using X-ray crystallography, we demonstrate that ribonuclease A (RNase A) undergoes significant domain motions upon ligand binding ...

    Despite the increasing number of successful determinations of complex protein structures the understanding of their dynamics properties is still rather limited. Using X-ray crystallography, we demonstrate that ribonuclease A (RNase A) undergoes significant domain motions upon ligand binding. In particular, when cytidine 2'-monophosphate binds to RNase A, the structure of the enzyme becomes more compact. Interestingly, our data also show that these structural alterations are fully reversible in the crystal state. These findings provide structural bases for the dynamic behavior of RNase A in the binding of the substrate shown by Petsko and coworkers (Rasmussen et al. Nature 1992;357:423-424). These subtle domain motions may assume functional relevance for more complex system and may play a significant role in the cooperativity of oligomeric enzymes.


    Related Citations: 
    • Productive and Non-Productive Binding to Ribonuclease A: X-Ray Structure of Two Complexes with Uridylyl(2',5')Guanosine
      Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L.
      (2000) Protein Sci 6: 1217
    • Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine
      Vitagliano, L., Adinolfi, S., Riccio, A., Sica, F., Zagari, A., Mazzarella, L.
      (1998) Protein Sci 7: 1691

    Organizational Affiliation

    Centro di Biocristallografia, CNR, Napoli, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE AAB124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2P
Query on C2P

Download CCD File 
A
CYTIDINE-2'-MONOPHOSPHATE
C9 H14 N3 O8 P
YQUAKORMLHPSLZ-XVFCMESISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C2PKi:  7000   nM  BindingDB
C2PKi :  7000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.08α = 90
b = 33.43β = 90.9
c = 73.22γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance