5DSU

Crystal structure of double mutant of N-domain of human calmodulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

On the Ca(2+) binding and conformational change in EF-hand domains: Experimental evidence of Ca(2+)-saturated intermediates of N-domain of calmodulin.

Ababou, A.Zaleska, M.Pfuhl, M.

(2017) Biochim Biophys Acta 1865: 640-651

  • DOI: https://doi.org/10.1016/j.bbapap.2017.03.003
  • Primary Citation of Related Structures:  
    5DSU

  • PubMed Abstract: 

    Double mutation of Q41L and K75I in the N-domain of calmodulin (N-Cam) stabilizes the closed form of N-Cam such that binding of Ca 2+ in solution no longer triggers a conformational change to the open form, and its Ca 2+ binding affinity decreases dramatically. To further investigate the solvation effects on the structure, Ca 2+ binding affinity and conformational dynamics of this N-Cam double mutant in the Ca 2+ saturated state, we solved its X-ray structure. Surprisingly, the structure revealed an open conformation of the domain which contradicts its closed conformation in solution. Here we provide evidence that crystallization conditions were responsible for this Ca 2+ -saturated domain open conformation in the crystal. Importantly, we demonstrate that the presence of the crystallization co-precipitant and alcohols were able to induce a progressive opening of the closed form of this domain, in Ca 2+ saturated state, in solution. However, in the Ca 2+ depleted state, addition of alcohols was unable to induce any opening of this domain in solution. In addition, in the Ca 2+ saturated state, the molecular dynamics simulations show that while N-Cam can populate the open and closed conformation, the N-Cam double mutant exclusively populates the closed conformation. Our results provide experimental evidence of intermediate conformations of Ca 2+ -saturated N-Cam in solution. We propose that conformational change of Ca 2+ sensor EF-hand domains depends on solvation energetics, Ca 2+ binding to promote the full open form, Ca 2+ depleted state conformational dynamics, and the chemical properties of the molecules nearby key residues such as those at positions 41 and 75 in N-Cam.


  • Organizational Affiliation

    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK; University of East London, School of Health, Sport and Bioscience, Water Lane, London E15 4LZ, UK. Electronic address: a.ababou10@yahoo.co.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin78Homo sapiensMutation(s): 3 
Gene Names: 
CALM1CALMCAMCAM1CALM2CAM2CAMBCALM3CALML2CAM3...
CALM1CALMCAMCAM1CALM2CAM2CAMBCALM3CALML2CAM3CAMCCAMIII

UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.4α = 90
b = 38.4β = 90
c = 81.2γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-04-12
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description