5E22

The second PDZ domain of Ligand of Numb protein X 2 in the presence of an electric field of ~1 MV/cm along the crystallographic x axis, with eightfold extrapolation of structure factor differences.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.797 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Electric-field-stimulated protein mechanics.

Hekstra, D.R.White, K.I.Socolich, M.A.Henning, R.W.Srajer, V.Ranganathan, R.

(2016) Nature 540: 400-405

  • DOI: 10.1038/nature20571
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The internal mechanics of proteins-the coordinated motions of amino acids and the pattern of forces constraining these motions-connects protein structure to function. Here we describe a new method combining the application of strong electric field pu ...

    The internal mechanics of proteins-the coordinated motions of amino acids and the pattern of forces constraining these motions-connects protein structure to function. Here we describe a new method combining the application of strong electric field pulses to protein crystals with time-resolved X-ray crystallography to observe conformational changes in spatial and temporal detail. Using a human PDZ domain (LNX2PDZ2) as a model system, we show that protein crystals tolerate electric field pulses strong enough to drive concerted motions on the sub-microsecond timescale. The induced motions are subtle, involve diverse physical mechanisms, and occur throughout the protein structure. The global pattern of electric-field-induced motions is consistent with both local and allosteric conformational changes naturally induced by ligand binding, including at conserved functional sites in the PDZ domain family. This work lays the foundation for comprehensive experimental study of the mechanical basis of protein function.


    Organizational Affiliation

    Green Center for Systems Biology, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ligand of Numb protein X 2
B, A
95Homo sapiensMutation(s): 1 
Gene Names: LNX2 (PDZRN1)
Find proteins for Q8N448 (Homo sapiens)
Go to Gene View: LNX2
Go to UniProtKB:  Q8N448
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.797 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.289 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.146α = 113.31
b = 38.146β = 113.31
c = 39.010γ = 62.28
Software Package:
Software NamePurpose
Epinormdata reduction
Precognitiondata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Robert A. Welch FoundationUnited StatesI-1366

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description