2GUD

Crystal structure of a complex of griffithsin with mannose at 0.94 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 

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This is version 1.3 of the entry. See complete history. 


Literature

Domain-swapped structure of the potent antiviral protein griffithsin and its mode of carbohydrate binding.

Ziolkowska, N.E., O'keefe, B.R., Mori, T., Zhu, C., Giomarelli, B., Vojdani, F., Palmer, K.E., McMahon, J.B., Wlodawer, A.

(2006) Structure 14: 1127-1135

  • DOI: 10.1016/j.str.2006.05.017
  • Primary Citation of Related Structures:  
    2GTY, 2GUC, 2GUD, 2GUE, 2GUX

  • PubMed Abstract: 

    • The crystal structure of griffithsin, an antiviral lectin from the red alga Griffithsia sp., was solved and refined at 1.3 A resolution for the free protein and 0.94 A for a complex with mannose. Griffithsin molecules form a domain-swapped dimer, in which two beta strands of one molecule complete a beta prism consisting of three four-stranded sheets, with an approximate 3-fold axis, of another molecule ...

    The crystal structure of griffithsin, an antiviral lectin from the red alga Griffithsia sp., was solved and refined at 1.3 A resolution for the free protein and 0.94 A for a complex with mannose. Griffithsin molecules form a domain-swapped dimer, in which two beta strands of one molecule complete a beta prism consisting of three four-stranded sheets, with an approximate 3-fold axis, of another molecule. The structure of each monomer bears close resemblance to jacalin-related lectins, but its dimeric structure is unique. The structures of complexes of griffithsin with mannose and N-acetylglucosamine defined the locations of three almost identical carbohydrate binding sites on each monomer. We have also shown that griffithsin is a potent inhibitor of the coronavirus responsible for severe acute respiratory syndrome (SARS). Antiviral potency of griffithsin is likely due to the presence of multiple, similar sugar binding sites that provide redundant attachment points for complex carbohydrate molecules present on viral envelopes.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
griffithsinA, B122GriffithsiaMutation(s): 0 
UniProt
Find proteins for P84801 (Griffithsia sp. (strain Q66D336))
Explore P84801 
Go to UniProtKB:  P84801
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84801
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.74α = 90
b = 39.44β = 91
c = 57.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary