4FUM

Structural basis for Zn2+-dependent intercellular adhesion in staphylococcal biofilms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for Zn2+-dependent intercellular adhesion in staphylococcal biofilms.

Conrady, D.G.Wilson, J.J.Herr, A.B.

(2013) Proc Natl Acad Sci U S A 110: E202-E211

  • DOI: https://doi.org/10.1073/pnas.1208134110
  • Primary Citation of Related Structures:  
    4FUM, 4FUN, 4FUO, 4FUP

  • PubMed Abstract: 

    Staphylococcal bacteria, including Staphylococcus epidermidis and Staphylococcus aureus, cause chronic biofilm-related infections. The homologous proteins Aap and SasG mediate biofilm formation in S. epidermidis and S. aureus, respectively. The self-association of these proteins in the presence of Zn(2+) leads to the formation of extensive adhesive contacts between cells. This study reports the crystal structure of a Zn(2+) -bound construct from the self-associating region of Aap. Several unusual structural features include elongated β-sheets that are solvent-exposed on both faces and the lack of a canonical hydrophobic core. Zn(2+)-dependent dimers are observed in three distinct crystal forms, formed via pleomorphic coordination of Zn(2+) in trans across the dimer interface. These structures illustrate how a long, flexible surface protein is able to form tight intercellular adhesion sites under adverse environmental conditions.


  • Organizational Affiliation

    Department of Molecular Genetics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Accumulation associated protein208Staphylococcus epidermidis RP62AMutation(s): 4 
Gene Names: aapSERP2398
UniProt
Find proteins for Q5HKE8 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A))
Explore Q5HKE8 
Go to UniProtKB:  Q5HKE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HKE8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.721α = 90
b = 33.637β = 121.06
c = 81.325γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary