1JK4

DES 1-6 BOVINE NEUROPHYSIN II COMPLEX WITH VASOPRESSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of an Unliganded Neurophysin and its Vasopressin Complex: Implications for Binding and Allosteric Mechanisms

Wu, C.K.Hu, B.Rose, J.P.Liu, Z.J.Nguyen, T.L.Zeng, C.Breslow, E.Wang, B.C.

(2001) Protein Sci 10: 1869-1880

  • DOI: https://doi.org/10.1110/ps.10601
  • Primary Citation of Related Structures:  
    1JK4, 1JK6

  • PubMed Abstract: 

    The structures of des 1-6 bovine neurophysin-II in the unliganded state and as its complex with lysine vasopressin were determined crystallographically at resolutions of 2.4 A and 2.3 A, respectively. The structure of the protein component of the vasopressin complex was, with some local differences, similar to that determined earlier of the full-length protein complexed with oxytocin, but relatively large differences, probably intrinsic to the hormones, were observed between the structures of bound oxytocin and bound vasopressin at Gln 4. The structure of the unliganded protein is the first structure of an unliganded neurophysin. Comparison with the liganded state indicated significant binding-induced conformational changes that were the largest in the loop region comprising residues 50-58 and in the 7-10 region. A subtle binding-induced tightening of the subunit interface of the dimer also was shown, consistent with a role for interface changes in neurophysin allosteric mechanism, but one that is probably not predominant. Interface changes are suggested to be communicated from the binding site through the strands of beta-sheet that connect these two regions, in part with mediation by Gly 23. Comparison of unliganded and liganded states additionally reveals that the binding site for the hormone alpha-amino group is largely preformed and accessible in the unliganded state, suggesting that it represents the initial site of hormone protein recognition. The potential molecular basis for its thermodynamic contribution to binding is discussed.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEUROPHYSIN 289Bos taurusMutation(s): 0 
UniProt
Find proteins for P01180 (Bos taurus)
Explore P01180 
Go to UniProtKB:  P01180
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01180
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lys Vasopressin9N/AMutation(s): 0 
UniProt
Find proteins for P01180 (Bos taurus)
Explore P01180 
Go to UniProtKB:  P01180
Entity Groups  
UniProt GroupP01180
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.9α = 90
b = 50.9β = 90
c = 105.8γ = 120
Software Package:
Software NamePurpose
MAR345data collection
X-GENdata reduction
AMoREphasing
X-PLORrefinement
X-GENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-04
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description