2OMX

Crystal structure of InlA S192N G194S+S/hEC1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Thermodynamically reengineering the listerial invasion complex InlA/E-cadherin.

Wollert, T., Heinz, D.W., Schubert, W.D.

(2007) Proc Natl Acad Sci U S A 104: 13960-13965

  • DOI: 10.1073/pnas.0702199104
  • Primary Citation of Related Structures:  
    2OMU, 2OMT, 2OMZ, 2OMX

  • PubMed Abstract: 

    • Biological processes essentially all depend on the specific recognition between macromolecules and their interaction partners. Although many such interactions have been characterized both structurally and biophysically, the thermodynamic effects of small ...

    Biological processes essentially all depend on the specific recognition between macromolecules and their interaction partners. Although many such interactions have been characterized both structurally and biophysically, the thermodynamic effects of small atomic changes remain poorly understood. Based on the crystal structure of the bacterial invasion protein internalin (InlA) of Listeria monocytogenes in complex with its human receptor E-cadherin (hEC1), we analyzed the interface to identify single amino acid substitutions in InlA that would potentially improve the overall quality of interaction and hence increase the weak binding affinity of the complex. Dissociation constants of InlA-variant/hEC1 complexes, as well as enthalpy and entropy of binding, were quantified by isothermal titration calorimetry. All single substitutions indeed significantly increase binding affinity. Structural changes were verified crystallographically at < or =2.0-A resolution, allowing thermodynamic characteristics of single substitutions to be rationalized structurally and providing unique insights into atomic contributions to binding enthalpy and entropy. Structural and thermodynamic data of all combinations of individual substitutions result in a thermodynamic network, allowing the source of cooperativity between distant recognition sites to be identified. One such pair of single substitutions improves affinity 5,000-fold. We thus demonstrate that rational reengineering of protein complexes is possible by making use of physically distant hot spots of recognition.

    Organizational Affiliation: 

    Molecular Host-Pathogen Interactions, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Internalin-A A462Listeria monocytogenes EGD-eMutation(s): 3 
Gene Names: inlA
Find proteins for A4GWL5 (Listeria monocytogenes)
Explore A4GWL5 
Go to UniProtKB:  A4GWL5
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Epithelial-cadherin B108Homo sapiensMutation(s): 0 
Gene Names: CDH1, CDHE, UVO
Find proteins for P12830 (Homo sapiens)
Explore P12830 
Go to UniProtKB:  P12830
NIH Common Fund Data Resources
PHAROS:  P12830
GTEx:  ENSG00000039068
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.887α = 74.75
b = 54.16β = 80.69
c = 68.811γ = 67.71
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Advisory, Refinement description