4HR6

Crystal structure of snake gourd (Trichosanthes anguina) seed lectin, a three chain homologue of type II RIPs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history


Literature

The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs.

Sharma, A.Pohlentz, G.Bobbili, K.B.Jeyaprakash, A.A.Chandran, T.Mormann, M.Swamy, M.J.Vijayan, M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1493-1503

  • DOI: 10.1107/S0907444913010020
  • Primary Citation of Related Structures:  
    4HR6

  • PubMed Abstract: 
  • The sequence and structure of snake gourd seed lectin (SGSL), a nontoxic homologue of type II ribosome-inactivating proteins (RIPs), have been determined by mass spectrometry and X-ray crystallography, respectively. As in type II RIPs, the molecule consists of a lectin chain made up of two β-trefoil domains ...

    The sequence and structure of snake gourd seed lectin (SGSL), a nontoxic homologue of type II ribosome-inactivating proteins (RIPs), have been determined by mass spectrometry and X-ray crystallography, respectively. As in type II RIPs, the molecule consists of a lectin chain made up of two β-trefoil domains. The catalytic chain, which is connected through a disulfide bridge to the lectin chain in type II RIPs, is cleaved into two in SGSL. However, the integrity of the three-dimensional structure of the catalytic component of the molecule is preserved. This is the first time that a three-chain RIP or RIP homologue has been observed. A thorough examination of the sequence and structure of the protein and of its interactions with the bound methyl-α-galactose indicate that the nontoxicity of SGSL results from a combination of changes in the catalytic and the carbohydrate-binding sites. Detailed analyses of the sequences of type II RIPs of known structure and their homologues with unknown structure provide valuable insights into the evolution of this class of proteins. They also indicate some variability in carbohydrate-binding sites, which appears to contribute to the different levels of toxicity exhibited by lectins from various sources.


    Related Citations: 
    • Crystallization and preliminary X-ray studies of snake gourd lectin: homology with type II ribosome-inactivating proteins.
      Manoj, N., Jeyaprakash, A.A., Pratap, J.V., Komath, S.S., Kenoth, R., Swamy, M.J., Vijayan, M.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 912

    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, Karnataka, India.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LECTIN A41Trichosanthes anguinaMutation(s): 0 
Find proteins for U3KRF6 (Trichosanthes anguina)
Explore U3KRF6 
Go to UniProtKB:  U3KRF6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LECTIN B206Trichosanthes anguinaMutation(s): 0 
Find proteins for U3KRF8 (Trichosanthes anguina)
Explore U3KRF8 
Go to UniProtKB:  U3KRF8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LECTIN C264Trichosanthes anguinaMutation(s): 0 
Find proteins for U3KRF8 (Trichosanthes anguina)
Explore U3KRF8 
Go to UniProtKB:  U3KRF8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMG
Query on AMG

Download Ideal Coordinates CCD File 
C
methyl alpha-D-galactopyranoside
C7 H14 O6
HOVAGTYPODGVJG-PZRMXXKTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.081α = 90
b = 102.081β = 90
c = 271.64γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary