5E21

PDZ2 of LNX2 at 277K,single conformer model

• PDB DOI: https://doi.org/10.2210/pdb5E21/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-09-30 Released: 2016-12-07 
• Deposition Author(s): Hekstra, D.R., White, K.I., Socolich, M.A., Ranganathan, R.
• Funding Organization(s): Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.140 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 

Starting Model: experimental

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

• PubMed: 27926732 
• DOI: https://doi.org/10.1038/nature20571
• Primary Citation of Related Structures:  
  5E11, 5E1Y, 5E21, 5E22


• 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 pulses to protein crystals with time-resolved X-ray crystallography to observe conformational changes in spatial and temporal detail. Using a human PDZ domain (LNX2 ^PDZ2 ) 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 10.31 kDa 
• Atom Count: 824 
• Modelled Residue Count: 95 
• Deposited Residue Count: 95 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligand of Numb protein X 2	A	95	Homo sapiens	Mutation(s): 1  Gene Names: LNX2, PDZRN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N448 (Homo sapiens) Explore Q8N448  Go to UniProtKB:  Q8N448
PHAROS:  Q8N448 GTEx:  ENSG00000139517

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.140 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.912	α = 90
b = 39.288	β = 117.41
c = 38.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Hekstra, D.R., White, K.I., Socolich, M.A., Ranganathan, R.

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Funding Organization	Location	Grant Number
Robert A. Welch Foundation	United States	I-1366

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-01-11
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description