4XCP | pdb_00004xcp

Fatty Acid and Retinol binding protein Na-FAR-1 from Necator americanus

• PDB DOI: https://doi.org/10.2210/pdb4XCP/pdb

• Classification: retinol-binding protein
• Organism(s): Necator americanus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-18 Released: 2015-09-16 
• Deposition Author(s): Gabrielsen, M., Rey-Burusco, M.F., Ibanez-Shimabukuro, M., Griffiths, K., Kennedy, M.W., Corsico, B., Smith, B.O.
• Funding Organization(s): Wellcome Trust, National Research Council of Argentina, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.222 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus.

Rey-Burusco, M.F., Ibanez-Shimabukuro, M., Gabrielsen, M., Franchini, G.R., Roe, A.J., Griffiths, K., Zhan, B., Cooper, A., Kennedy, M.W., Corsico, B., Smith, B.O.

(2015) Biochem J 471: 403-414

• PubMed: 26318523 
• DOI: https://doi.org/10.1042/BJ20150068
• Primary Citation Related Structures: 
  4UET, 4XCP


• PubMed Abstract: 
  

  Fatty acid and retinol-binding proteins (FARs) comprise a family of unusual α-helix rich lipid-binding proteins found exclusively in nematodes. They are secreted into host tissues by parasites of plants, animals and humans. The structure of a FAR protein from the free-living nematode Caenorhabditis elegans is available, but this protein [C. elegans FAR-7 (Ce-FAR-7)] is from a subfamily of FARs that does not appear to be important at the host/parasite interface. We have therefore examined [Necator americanus FAR-1 (Na-FAR-1)] from the blood-feeding intestinal parasite of humans, N. americanus. The 3D structure of Na-FAR-1 in its ligand-free and ligand-bound forms, determined by NMR (nuclear magnetic resonance) spectroscopy and X-ray crystallography respectively, reveals an α-helical fold similar to Ce-FAR-7, but Na-FAR-1 possesses a larger and more complex internal ligand-binding cavity and an additional C-terminal α-helix. Titration of apo-Na-FAR-1 with oleic acid, analysed by NMR chemical shift perturbation, reveals that at least four distinct protein-ligand complexes can be formed. Na-FAR-1 and possibly other FARs may have a wider repertoire for hydrophobic ligand binding, as confirmed in the present study by our finding that a range of neutral and polar lipids co-purify with the bacterially expressed recombinant protein. Finally, we show by immunohistochemistry that Na-FAR-1 is present in adult worms with a tissue distribution indicative of possible roles in nutrient acquisition by the parasite and in reproduction in the male.

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Organizational Affiliation: 
• Instituto de Investigaciones Bioquímicas de La Plata, CONICET-UNLP, Facultad de Ciencias Médicas, calles 60 y 120, 1900-La Plata, Argentina.
Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, U.K.
Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, U.K.
National School of Tropical Medicine and Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine, Houston, TX 20031, U.S.A.
School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, U.K. Institute of Molecular, Cell & Systems Biology, University of Glasgow, Glasgow G12 8QQ, U.K. [e-mail] [e-mail].
Institute of Molecular, Cell & Systems Biology, University of Glasgow, Glasgow G12 8QQ, U.K. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.55 kDa 
• Atom Count: 1,385 
• Modeled Residue Count: 155 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nematode fatty acid retinoid binding protein	A	170	Necator americanus	Mutation(s): 0  Gene Names: NECAME_14208
UniProt
Find proteins for W2SRJ3 (Necator americanus) Explore W2SRJ3  Go to UniProtKB:  W2SRJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	B [auth A], C [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.222 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.123	α = 90
b = 121.123	β = 90
c = 121.123	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Gabrielsen, M., Rey-Burusco, M.F., Ibanez-Shimabukuro, M., Griffiths, K., Kennedy, M.W., Corsico, B., Smith, B.O.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	083625
National Research Council of Argentina	Argentina	--
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/G011389/1

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Author supporting evidence
• Version 1.3: 2017-08-30
  Changes: Author supporting evidence
• Version 2.0: 2024-10-23
  Changes: Atomic model, Data collection, Database references, Structure summary