1CB1

THREE-DIMENSIONAL SOLUTION STRUCTURE OF CA2+-LOADED PORCINE CALBINDIN D9K DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 13 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy.

Akke, M.Drakenberg, T.Chazin, W.J.

(1992) Biochemistry 31: 1011-1020

  • DOI: 10.1021/bi00119a009
  • Primary Citation of Related Structures:  
    1CB1

  • PubMed Abstract: 
  • The three-dimensional solution structure of native, intact porcine calbindin D9k has been determined by distance geometry and restrained molecular dynamics calculations using distance and dihedral angle constraints obtained from 1H NMR spectroscopy. The protein has a well-defined global fold consisting of four helices oriented in a pairwise antiparallel manner such that two pairs of helix-loop-helix motifs (EF-hands) are joined by a linker segment ...

    The three-dimensional solution structure of native, intact porcine calbindin D9k has been determined by distance geometry and restrained molecular dynamics calculations using distance and dihedral angle constraints obtained from 1H NMR spectroscopy. The protein has a well-defined global fold consisting of four helices oriented in a pairwise antiparallel manner such that two pairs of helix-loop-helix motifs (EF-hands) are joined by a linker segment. The two EF-hands are further coupled through a short beta-type interaction between the two Ca(2+)-binding loops. Overall, the structure is very similar to that of the highly homologous native, minor A form of bovine calbindin D9k determined by X-ray crystallography [Szebenyi, D. M. E., & Moffat, K. (1986) J. Biol. Chem. 261, 8761-8776]. A model structure built from the bovine calbindin D9k crystal structure shows several deviations larger than 2 A from the experimental distance constraints for the porcine protein. These structural differences are efficiently removed by subjecting the model structure to the experimental distance and dihedral angle constraints in a restrained molecular dynamics protocol, thereby generating a model that is very similar to the refined distance geometry derived structures. The N-terminal residues of the intact protein that are absent in the minor A form appear to be highly flexible and do not influence the structure of other regions of the protein. This result is important because it validates the conclusions drawn from the wide range of studies that have been carried out on minor A forms rather than the intact calbindin D9k.


    Related Citations: 
    • 1H NMR Studies of Porcine Calbindin D9K in Solution: Sequential Resonance Assignment, Secondary Structure, and Global Fold
      Drakenberg, T., Hofmann, T., Chazin, W.J.
      (1989) Biochemistry 28: 5946

    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CALBINDIN D9KA78Sus scrofaMutation(s): 0 
Gene Names: S100GCALB3S100D
UniProt
Find proteins for P02632 (Sus scrofa)
Explore P02632 
Go to UniProtKB:  P02632
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02632
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 13 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Database references, Derived calculations, Other