5D55 | pdb_00005d55

Crystal structure of the E. coli Hda pilus minor tip subunit, HdaB

• PDB DOI: https://doi.org/10.2210/pdb5D55/pdb

• Classification: CELL ADHESION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-10 Released: 2016-08-10 
• Deposition Author(s): Lee, W.-C., Garnett, J.A., Matthews, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and analysis of HdaB: The enteroaggregative Escherichia coli AAF/IV pilus tip protein.

Lee, W.C., Matthews, S., Garnett, J.A.

(2016) Protein Sci 25: 1898-1905

• PubMed: 27400770 
• DOI: https://doi.org/10.1002/pro.2982
• Primary Citation Related Structures: 
  5D55


• PubMed Abstract: 
  

  Enteroaggregative Escherichia coli is the primary cause of pediatric diarrhea in developing countries. They utilize aggregative adherence fimbriae (AAFs) to promote initial adherence to the host intestinal mucosa, promote the formation of biofilms, and mediate host invasion. Five AAFs have been identified to date and AAF/IV is amongst the most prevalent found in clinical isolates. Here we present the X-ray crystal structure of the AAF/IV tip protein HdaB at 2.0 Å resolution. It shares high structural homology with members of the Afa/Dr superfamily of fimbriae, which are involved in host invasion. We highlight surface exposed residues that share sequence homology and propose that these may function in invasion and also non-conserved regions that could mediate HdaB specific adhesive functions.

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Organizational Affiliation: 
• Department of Life Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom.
School of Biological and Chemical Sciences, Queen Mary University London, London, E1 4NS, United Kingdom. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.67 kDa 
• Atom Count: 2,483 
• Modeled Residue Count: 290 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HdaB,HdaA (Adhesin), HUS-associated diffuse adherence	A, B	157	Escherichia coli	Mutation(s): 0  Gene Names: hdaB, hdaA
UniProt
Find proteins for B3V224 (Escherichia coli) Explore B3V224  Go to UniProtKB:  B3V224
Find proteins for Q08JP6 (Escherichia coli) Explore Q08JP6  Go to UniProtKB:  Q08JP6
UniProt Groups	Q08JP6B3V224

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A], D [auth B], E [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
IOD	F [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.294	α = 90
b = 112.294	β = 90
c = 61.652	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Lee, W.-C., Garnett, J.A., Matthews, S.J.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary