3HNX

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

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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 ...

    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.

    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
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyanovirin-N-like proteinA110Tuber borchii, Neurospora crassaMutation(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
Protein Feature View
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  • Reference Sequence
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 = 45.506α = 90
b = 46.204β = 90
c = 50.377γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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