3OBL | pdb_00003obl

Crystal structure of the potent anti-HIV cyanobacterial lectin from Oscillatoria Agardhii

• PDB DOI: https://doi.org/10.2210/pdb3OBL/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Planktothrix agardhii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-06 Released: 2010-10-20 
• Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.169 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.157 (DCC) 

Literature

Novel fold and carbohydrate specificity of the potent anti-HIV cyanobacterial lectin from Oscillatoria agardhii.

Koharudin, L.M., Furey, W., Gronenborn, A.M.

(2011) J Biological Chem 286: 1588-1597

• PubMed: 20961847 
• DOI: https://doi.org/10.1074/jbc.M110.173278
• Primary Citation Related Structures: 
  3OBL


• PubMed Abstract: 
  

  Oscillatoria agardhii agglutinin (OAA) is a recently discovered cyanobacterial lectin that exhibits potent anti-HIV activity. Up to now, only its primary structure and carbohydrate binding data have been available. To elucidate the structural basis for the antiviral mechanism of OAA, we determined the structure of this lectin by x-ray crystallography at 1.2 Å resolution and mapped the specific carbohydrate recognition sites of OAA by NMR spectroscopy. The overall architecture of OAA comprises 10 β-strands that fold into a single, compact, β-barrel-like domain, creating a unique topology compared with all known protein structures in the Protein Data Bank. OAA sugar binding was tested against Man-9 and various disaccharide components of Man-9. Two symmetric carbohydrate-binding sites were located on the protein, and a preference for Manα(1-6)Man-linked sugars was found. Altogether, our structural results explain the antiviral activity OAA and add to the growing body of knowledge about antiviral lectins.

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Organizational Affiliation: 
• Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.75 kDa 
• Atom Count: 2,524 
• Modeled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	132	Planktothrix agardhii	Mutation(s): 0  Gene Names: OAA
UniProt
Find proteins for C0STD7 (Planktothrix agardhii) Explore C0STD7  Go to UniProtKB:  C0STD7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	C [auth A], D [auth A], E [auth B], F [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.169 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.157 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.752	α = 78.16
b = 47.275	β = 62.99
c = 47.367	γ = 63.14

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHENIX	model building
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations