4G7Y | pdb_00004g7y

Crystal structure of voltage sensing domain of Ci-VSP with fragment antibody (R217E, 2.8 A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.

Li, Q.Wanderling, S.Paduch, M.Medovoy, D.Singharoy, A.McGreevy, R.Villalba-Galea, C.A.Hulse, R.E.Roux, B.Schulten, K.Kossiakoff, A.Perozo, E.

(2014) Nat Struct Mol Biol 21: 244-252

  • DOI: https://doi.org/10.1038/nsmb.2768
  • Primary Citation of Related Structures:  
    4G7V, 4G7Y, 4G80

  • PubMed Abstract: 

    The transduction of transmembrane electric fields into protein motion has an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSDs) carry out these functions through reorientations of positive charges in the S4 helix. Here, we determined crystal structures of the Ciona intestinalis VSD (Ci-VSD) in putatively active and resting conformations. S4 undergoes an ~5-Å displacement along its main axis, accompanied by an ~60° rotation. This movement is stabilized by an exchange in countercharge partners in helices S1 and S3 that generates an estimated net charge transfer of ~1 eo. Gating charges move relative to a ''hydrophobic gasket' that electrically divides intra- and extracellular compartments. EPR spectroscopy confirms the limited nature of S4 movement in a membrane environment. These results provide an explicit mechanism for voltage sensing and set the basis for electromechanical coupling in voltage-dependent enzymes and ion channels.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fragment antibody heavy chainA [auth H]219Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fragment antibody light chainB [auth L]211Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-sensor containing phosphataseC [auth S]185Ciona intestinalisMutation(s): 1 
Gene Names: Ci-VSP
Membrane Entity: Yes 
UniProt
Find proteins for Q4W8A1 (Ciona intestinalis)
Explore Q4W8A1 
Go to UniProtKB:  Q4W8A1
Entity Groups  
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UniProt GroupQ4W8A1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.01α = 90
b = 121.01β = 90
c = 229.57γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
JBlucedata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LDAClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2014-02-05 
  • Deposition Author(s): Li, Q.

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2017-12-13
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary