Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 12.39 kDa 
• Atom Count: 1083 
• Modelled Residue Count: 108 
• Deposited Residue Count: 110 
• Unique protein chains: 1

3HNX

Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG in P212121 space group

• PDB DOI: 10.2210/pdb3HNX/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Tuber borchii, Neurospora crassa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-01 Released: 2009-06-23 
• Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.210 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

A designed chimeric cyanovirin-N homolog lectin: Structure and molecular basis of sucrose binding.

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

(2009) Proteins 77: 904-915

• PubMed: 19639634 
• DOI: 10.1002/prot.22514
• Primary Citation of Related Structures:  
  3HNU, 3HNX, 3HP8


• PubMed Abstract: 
  

The NMR and X-ray structures of a designed chimeric cyanovirin-N homolog (CVNH) protein were determined. The individual halves of the structure are similar to their counterparts in the parent proteins, with domains A and B resembling the structures of TbCVNH and NcCVNH, respectively. No significant differences between the solution and crystal conformations were observed, although details in loop conformations and distinct crystal packing-induced features are present. Carbohydrate binding studies by NMR revealed affinity and specificity for Glc alpha(1-2)Frc and Man alpha(1-2)Man, and the parental half that is devoid of any sucrose affinity in NcCVNH was transformed into a genuine sucrose binding site in the context of the chimera. The atomic details of sugar recognition are seen in the crystal structure of the protein with two bound Glc alpha(1-2)Frc molecules. Both sugars exhibit different conformations around the glycosidic bond and engage in unique hydrogen bonding networks in the two sites. Although the protein is able to bind two Man alpha(1-2)Man molecules, a property associated with HIV-inactivation, no anti-HIV activity was observed for the hybrid protein. These results provide the structural basis for sugar recognition in the CVNH family and aid in deciphering the relationship between sugar binding and anti-HIV activity.

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Related Citations: 

• The Evolutionarily Conserved Family of Cyanovirin-N Homologs: Structures and Carbohydrate Specificity
  Koharudin, L.M.I., Viscomi, A., Jee, J., Ottonello, S., Gronenborn, A.M.
  (2008) Structure 16: 570

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Organizational Affiliation: 

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanovirin-N-like protein	A	110	Tuber borchii, Neurospora crassa	Mutation(s): 0
UniProt
Find proteins for Q5MK11 (Tuber borchii) Explore Q5MK11  Go to UniProtKB:  Q5MK11
Find proteins for Q7S6U4 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q7S6U4  Go to UniProtKB:  Q7S6U4
UniProt Groups	Q5MK11Q7S6U4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.210 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.506	α = 90
b = 46.204	β = 90
c = 50.377	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-01 
• Released Date: 2009-06-23 
Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy