3GPR

Crystal structure of rhodocetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The alpha2beta1 integrin-specific antagonist rhodocetin is a cruciform, heterotetrameric molecule

Eble, J.A.Niland, S.Bracht, T.Mormann, M.Peter-Katalinic, J.Pohlentz, G.Stetefeld, J.

(2009) FASEB J 23: 2917-2927

  • DOI: 10.1096/fj.08-126763
  • Primary Citation of Related Structures:  
    3GPR

  • PubMed Abstract: 
  • The integrin alpha2beta1 plays an important role in various pathophysiological processes, such as thrombosis, wound healing, inflammation, and metastasis. Rhodocetin, a constituent of the venom of the hemorrhagic Malayan pit viper (Calloselasma rhodo ...

    The integrin alpha2beta1 plays an important role in various pathophysiological processes, such as thrombosis, wound healing, inflammation, and metastasis. Rhodocetin, a constituent of the venom of the hemorrhagic Malayan pit viper (Calloselasma rhodostoma), is a specific alpha2beta1 integrin antagonist. To understand its molecular mode of action, its structure was studied by crystallography. Its quaternary structure in solution was also analyzed biochemically. Two novel subunits of rhodocetin were sequenced by mass spectrometry. Their integrin binding was measured by protein interaction ELISAs. Rhodocetin is a C-type lectin-like protein (CLP) consisting of four homologous, yet distinct, subunits, alpha, beta, gamma, and delta, the latter two of which have been unknown to date. With their CLP folds and loop-swapping motifs, the subunits alpha, beta and gamma, delta form two heterodimeric pairs. Uniquely, they arrange orthogonally and shape a cruciform molecule. Bearing a single unpaired cysteine residue, rhodocetin can only form covalent supramolecular complexes with a maximum aggregation number of 2, unlike many heterodimeric CLPs. Being the first heterotetrameric CLP to be crystallized, rhodocetin provides not only the prototypic molecular structure for heterotetrameric CLPs, but also a lead structure for pharmaceutical alpha2beta1 integrin antagonists.


    Organizational Affiliation

    Center for Molecular Medicine, Department of Vascular Matrix Biology, Excellence Cluster Cardio-Pulmonary System, Frankfurt University Hospital, Frankfurt, Germany. eble@med.uni-frankfurt.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rhodocetin subunit alphaA133Calloselasma rhodostomaMutation(s): 0 
Find proteins for P81397 (Calloselasma rhodostoma)
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Go to UniProtKB:  P81397
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rhodocetin subunit betaB129Calloselasma rhodostomaMutation(s): 0 
Find proteins for P81398 (Calloselasma rhodostoma)
Explore P81398 
Go to UniProtKB:  P81398
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Rhodocetin subunit gammaC134Calloselasma rhodostomaMutation(s): 0 
Find proteins for D2YW39 (Calloselasma rhodostoma)
Explore D2YW39 
Go to UniProtKB:  D2YW39
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Rhodocetin subunit deltaD124Calloselasma rhodostomaMutation(s): 0 
Find proteins for D2YW40 (Calloselasma rhodostoma)
Explore D2YW40 
Go to UniProtKB:  D2YW40
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.546α = 90
b = 83.546β = 90
c = 196.078γ = 120
Software Package:
Software NamePurpose
PHASESphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-03-23 
  • Released Date: 2009-12-15 
  • Deposition Author(s): Stetefeld, J.

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance