1HD3

A-SPECTRIN SH3 DOMAIN F52Y MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unspecific Hydrophobic Stabilization of Folding Transition States

Viguera, A.R.Vega, C.Serrano, L.

(2002) Proc.Natl.Acad.Sci.USA 99: 5349

  • DOI: 10.1073/pnas.072387799

  • PubMed Abstract: 
  • Here we present a method for determining the inference of non-native conformations in the folding of a small domain, alpha-spectrin Src homology 3 domain. This method relies on the preservation of all native interactions after Tyr/Phe exchanges in so ...

    Here we present a method for determining the inference of non-native conformations in the folding of a small domain, alpha-spectrin Src homology 3 domain. This method relies on the preservation of all native interactions after Tyr/Phe exchanges in solvent-exposed, contact-free positions. Minor changes in solvent exposure and free energy of the denatured ensemble are in agreement with the reverse hydrophobic effect, as the Tyr/Phe mutations slightly change the polypeptide hydrophilic/hydrophobic balance. Interestingly, more important Gibbs energy variations are observed in the transition state ensemble (TSE). Considering the small changes induced by the H/OH replacements, the observed energy variations in the TSE are rather notable, but of a magnitude that would remain undetected under regular mutations that alter the folded structure free energy. Hydrophobic residues outside of the folding nucleus contribute to the stability of the TSE in an unspecific nonlinear manner, producing a significant acceleration of both unfolding and refolding rates, with little effect on stability. These results suggest that sectors of the protein transiently reside in non-native areas of the landscape during folding, with implications in the reading of phi values from protein engineering experiments. Contrary to previous proposals, the principle that emerges is that non-native contacts, or conformations, could be beneficial in evolution and design of some fast folding proteins.


    Related Citations: 
    • Crystal Structure of a Src-Homology 3 (SH3) Domain
      Musacchio, A.,Noble, M.,Pauptit, R.,Wierenga, R.,Saraste, M.
      (1992) Nature 359: 851


    Organizational Affiliation

    European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 10229, D-69012, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPECTRIN ALPHA CHAIN
A
62Gallus gallusGene Names: SPTAN1 (SPTA2)
Find proteins for P07751 (Gallus gallus)
Go to Gene View: SPTAN1
Go to UniProtKB:  P07751
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
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: 1.98 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.970α = 90.00
b = 42.370β = 90.00
c = 49.610γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance