2BL0

Physarum polycephalum myosin II regulatory domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Evidence for Non-Canonical Binding of Ca2+ to a Canonical EF-Hand of a Conventional Myosin.

Debreczeni, J.E.Farkas, L.Harmat, V.Hetenyi, C.Hajdu, I.Zavodszky, P.Kohama, K.Nyitray, L.

(2005) J Biol Chem 280: 41458

  • DOI: https://doi.org/10.1074/jbc.M506315200
  • Primary Citation of Related Structures:  
    2BL0

  • PubMed Abstract: 

    We have previously identified a single inhibitory Ca2+-binding site in the first EF-hand of the essential light chain of Physarum conventional myosin (Farkas, L., Malnasi-Csizmadia, A., Nakamura, A., Kohama, K., and Nyitray, L. (2003) J. Biol. Chem. 278, 27399-27405). As a general rule, conformation of the EF-hand-containing domains in the calmodulin family is "closed" in the absence and "open" in the presence of bound cations; a notable exception is the unusual Ca2+-bound closed domain in the essential light chain of the Ca2+-activated scallop muscle myosin. Here we have reported the 1.8 A resolution structure of the regulatory domain (RD) of Physarum myosin II in which Ca2+ is bound to a canonical EF-hand that is also in a closed state. The 12th position of the EF-hand loop, which normally provides a bidentate ligand for Ca2+ in the open state, is too far in the structure to participate in coordination of the ion. The structure includes a second Ca2+ that only mediates crystal contacts. To reveal the mechanism behind the regulatory effect of Ca2+, we compared conformational flexibilities of the liganded and unliganded RD. Our working hypothesis, i.e. the modulatory effect of Ca2+ on conformational flexibility of RD, is in line with the observed suppression of hydrogen-deuterium exchange rate in the Ca2+-bound form, as well as with results of molecular dynamics calculations. Based on this evidence, we concluded that Ca2+-induced change in structural dynamics of RD is a major factor in Ca2+-mediated regulation of Physarum myosin II activity.


  • Organizational Affiliation

    Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAJOR PLASMODIAL MYOSIN HEAVY CHAIN63Physarum polycephalumMutation(s): 0 
UniProt
Find proteins for Q9BJD3 (Physarum polycephalum)
Explore Q9BJD3 
Go to UniProtKB:  Q9BJD3
Entity Groups  
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UniProt GroupQ9BJD3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MYOSIN REGULATORY LIGHT CHAIN145Physarum polycephalumMutation(s): 0 
UniProt
Find proteins for P08053 (Physarum polycephalum)
Explore P08053 
Go to UniProtKB:  P08053
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UniProt GroupP08053
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MYOSIN REGULATORY LIGHT CHAIN142Physarum polycephalumMutation(s): 0 
UniProt
Find proteins for Q8WSQ4 (Physarum polycephalum)
Explore Q8WSQ4 
Go to UniProtKB:  Q8WSQ4
Entity Groups  
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UniProt GroupQ8WSQ4
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.574α = 90
b = 70.858β = 90
c = 97.877γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other