5HEB

The third PDZ domain from the synaptic protein PSD-95 in complex with a C-terminal peptide derived from CRIPT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Origins of Allostery and Evolvability in Proteins: A Case Study.

Raman, A.S.White, K.I.Ranganathan, R.

(2016) Cell 166: 468-480

  • DOI: 10.1016/j.cell.2016.05.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins display the capacity for adaptation to new functions, a property critical for evolvability. But what structural principles underlie the capacity for adaptation? Here, we show that adaptation to a physiologically distinct class of ligand spec ...

    Proteins display the capacity for adaptation to new functions, a property critical for evolvability. But what structural principles underlie the capacity for adaptation? Here, we show that adaptation to a physiologically distinct class of ligand specificity in a PSD95, DLG1, ZO-1 (PDZ) domain preferentially occurs through class-bridging intermediate mutations located distant from the ligand-binding site. These mutations provide a functional link between ligand classes and demonstrate the principle of "conditional neutrality" in mediating evolutionary adaptation. Structures show that class-bridging mutations work allosterically to open up conformational plasticity at the active site, permitting novel functions while retaining existing function. More generally, the class-bridging phenotype arises from mutations in an evolutionarily conserved network of coevolving amino acids in the PDZ family (the sector) that connects the active site to distant surface sites. These findings introduce the concept that allostery in proteins could have its origins not in protein function but in the capacity to adapt.


    Organizational Affiliation

    Green Center for Systems Biology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.,Green Center for Systems Biology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA; Departments of Biophysics and Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA. Electronic address: rama.ranganathan@utsouthwestern.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disks large homolog 4
A
119Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4 (Dlgh4, Psd95)
Find proteins for P31016 (Rattus norvegicus)
Go to UniProtKB:  P31016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cysteine-rich PDZ-binding protein
B
9Rattus norvegicusMutation(s): 0 
Gene Names: Cript
Find proteins for Q792Q4 (Rattus norvegicus)
Go to UniProtKB:  Q792Q4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, 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: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 89.771α = 90.00
b = 89.771β = 90.00
c = 89.771γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
Cootmodel building
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: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations