Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 26.69 kDa 
• Atom Count: 2256 
• Modelled Residue Count: 244 
• Deposited Residue Count: 244 
• Unique protein chains: 1

2NUO

Crystal structure of a complex of griffithsin with glucose

• PDB DOI: 10.2210/pdb2NUO/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Griffithsia
• Expression System: Nicotiana benthamiana
• Mutation(s): Yes 


• Deposited: 2006-11-09 Released: 2007-08-07 
• Deposition Author(s): Ziolkowska, N.E., Wlodawer, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.203 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

Crystallographic studies of the complexes of antiviral protein griffithsin with glucose and N-acetylglucosamine.

Ziolkowska, N.E., Shenoy, S.R., O'Keefe, B.R., Wlodawer, A.

(2007) Protein Sci 16: 1485-1489

• PubMed: 17567736 
• DOI: 10.1110/ps.072889407
• Primary Citation of Related Structures:  
  2NU5, 2NUO


• PubMed Abstract: 
  

Crystal structures of complexes of an antiviral lectin griffithsin (GRFT) with glucose and N-acetylglucosamine were solved and refined at high resolution. In both complexes, all six monosaccharide-binding sites of GRFT were occupied and the mode of binding was similar to that of mannose. In our previous attempts to obtain a complex with N-acetylglucosamine by soaking, only a single site was occupied; thus, cocrystallization was clearly superior despite lower concentration of the ligand. Isothermal titration calorimetric experiments with N-acetylglucosamine, glucose, and mannose provided enthalpic evidence of distinct binding differences between the three monosaccharides. A comparison of the mode of binding of different monosaccharides is discussed in the context of the antiviral activity of GRFT, based on specific binding to high-mannose-containing complex carbohydrates found on viral envelopes.

---

Organizational Affiliation: 

Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, NCI-Frederick, MD 21702-1201, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Griffithsin	A, B	122	Griffithsia	Mutation(s): 1
UniProt
Find proteins for P84801 (Griffithsia sp. (strain Q66D336)) Explore P84801  Go to UniProtKB:  P84801

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.203 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.49	α = 90
b = 53.67	β = 90
c = 103.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-09 
• Released Date: 2007-08-07 
Deposition Author(s): Ziolkowska, N.E., Wlodawer, A.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary