7KO9 | pdb_00007ko9

Crystal structure of antigen 43 from uropathogenic Escherichia coli UTI89


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms.

Vo, J.L.Ortiz, G.C.M.Totsika, M.Lo, A.W.Hancock, S.J.Whitten, A.E.Hor, L.Peters, K.M.Ageorges, V.Caccia, N.Desvaux, M.Schembri, M.A.Paxman, J.J.Heras, B.

(2022) NPJ Biofilms Microbiomes 8: 20-20

  • DOI: https://doi.org/10.1038/s41522-022-00284-1
  • Primary Citation Related Structures: 
    7KO9, 7KOB, 7KOH

  • PubMed Abstract: 

    The formation of aggregates and biofilms enhances bacterial colonisation and infection progression by affording protection from antibiotics and host immune factors. Despite these advantages there is a trade-off, whereby bacterial dissemination is reduced. As such, biofilm development needs to be controlled to suit adaptation to different environments. Here we investigate members from one of largest groups of bacterial adhesins, the autotransporters, for their critical role in the assembly of bacterial aggregates and biofilms. We describe the structural and functional characterisation of autotransporter Ag43 variants from different Escherichia coli pathotypes. We show that specific interactions between amino acids on the contacting interfaces of adjacent Ag43 proteins drives a common mode of trans-association that leads to cell clumping. Furthermore, subtle variation of these interactions alters aggregation kinetics and the degree of compacting within cell clusters. Together, our structure-function investigation reveals an underlying molecular basis for variations in the density of bacterial communities.


  • Organizational Affiliation
    • Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.

Macromolecule Content 

  • Total Structure Weight: 57.31 kDa 
  • Atom Count: 4,079 
  • Modeled Residue Count: 543 
  • Deposited Residue Count: 564 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AidA-I family adhesin564Escherichia coliMutation(s): 0 
Gene Names: fluAC789_1c11300CT146_19135EA231_25565HmCmsJML146_03717NCTC9434_03577
EC: 3.4.21
UniProt
Find proteins for Q1RDE2 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1RDE2 
Go to UniProtKB:  Q1RDE2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1RDE2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT

Query on CIT



Download:Ideal Coordinates CCD File
H [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.28α = 90
b = 132.82β = 94.13
c = 47.25γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia180102987
Australian Research Council (ARC)Australia150102287
National Health and Medical Research Council (NHMRC, Australia)Australia1143638

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description