1D1O | pdb_00001d1o

COOPERATIVITY IN EF-HAND CA2+-BINDING PROTEINS: EVIDENCE OF SITE-SITE COMMUNICATION FROM BINDING-INDUCED CHANGES IN STRUCTURE AND DYNAMICS OF N56A CALBINDIN D9K


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 24 
  • Selection Criteria: STRUCTURES WITH ACCEPTABLE MOLECULAR ENEGIES WERE ORDERED BY LEAST RESTRAINT VIOLATIONS. THE 24 BEST CONFORMERS WERE SELECTED TO FACILITATE COMPARISON TO PREVIOUS STRUCTURES OF THE PROTEIN AND BECAUSE THIS SURPASSES THE STATISTICAL REQUIREMENT TO REPRESENT ALL OF CONFORMATIONAL SPACE CONSISTENT WITH THE DATA. 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Site-site communication in the EF-hand Ca2+-binding protein calbindin D9k.

Maler, L.Blankenship, J.Rance, M.Chazin, W.J.

(2000) Nat Struct Biol 7: 245-250

  • DOI: https://doi.org/10.1038/73369
  • Primary Citation Related Structures: 
    1D1O

  • PubMed Abstract: 

    The cooperative binding of Ca2+ ions is an essential functional property of the EF-hand family of Ca2+-binding proteins. To understand how these proteins function, it is essential to characterize intermediate binding states in addition to the apo- and holo-proteins. The three-dimensional solution structure and fast time scale internal motional dynamics of the backbone have been determined for the half-saturated state of the N56A mutant of calbindin D9k with Ca2+ bound only in the N-terminal site. The extent of conformational reorganization and a loss of flexibility in the C-terminal EF-hand upon binding of an ion in the N-terminal EF-hand provide clear evidence of the importance of site-site interactions in this family of proteins, and demonstrates the strength of long-range effects in the cooperative EF-hand Ca2+-binding domain.


  • Organizational Affiliation
    • Department of Molecular Biology (MB9), The Scripps Research Institute, 10550 North Torrey Pines Road., La Jolla, California 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 8.5 kDa 
  • Atom Count: 598 
  • Modeled Residue Count: 75 
  • Deposited Residue Count: 75 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CALBINDIN D9K75Bos taurusMutation(s): 0 
UniProt
Find proteins for P02633 (Bos taurus)
Explore P02633 
Go to UniProtKB:  P02633
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02633
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 24 
  • Selection Criteria: STRUCTURES WITH ACCEPTABLE MOLECULAR ENEGIES WERE ORDERED BY LEAST RESTRAINT VIOLATIONS. THE 24 BEST CONFORMERS WERE SELECTED TO FACILITATE COMPARISON TO PREVIOUS STRUCTURES OF THE PROTEIN AND BECAUSE THIS SURPASSES THE STATISTICAL REQUIREMENT TO REPRESENT ALL OF CONFORMATIONAL SPACE CONSISTENT WITH THE DATA. 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-08
    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: 2022-02-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection