4FUP | pdb_00004fup

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.276 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4FUP

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 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.

Macromolecule Content 

  • Total Structure Weight: 44.9 kDa 
  • Atom Count: 2,933 
  • Modeled Residue Count: 394 
  • Deposited Residue Count: 416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Accumulation associated protein
A, B
208Staphylococcus 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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.276 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.101α = 90
b = 34.24β = 101.31
c = 138.779γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
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: 2024-02-28
    Changes: Data collection, Database references, Derived calculations