1JVU

CRYSTAL STRUCTURE OF RIBONUCLEASE A (COMPLEXED FORM)

• PDB DOI: https://doi.org/10.2210/pdb1JVU/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2001-08-31 Released: 2002-06-05 
• Deposition Author(s): Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L.

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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 

Starting Model: experimental

Literature

Reversible Substrate-Induced Domain Motions in Ribonuclease A

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

(2002) Proteins 46: 97-104

• PubMed: 11746706 
• DOI: https://doi.org/10.1002/prot.10033
• Primary Citation of Related Structures:  
  1JVT, 1JVU, 1JVV


• 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. 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.

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Organizational Affiliation: 

Centro di Biocristallografia, CNR, Napoli, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.74 kDa 
• Atom Count: 1,999 
• Modelled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE A	A, B	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2P	C [auth A]	CYTIDINE-2'-MONOPHOSPHATE C9 H14 N3 O8 P YQUAKORMLHPSLZ-XVFCMESISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C2P	BindingDB:  1JVU	Ki: 7000 (nM) from 1 assay(s)
	PDBBind:  1JVU	Ki: 7000 (nM) from 1 assay(s)

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 = 101.08	α = 90
b = 33.43	β = 90.9
c = 73.22	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-05 
Deposition Author(s): Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L.

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
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary