1IOA

ARCELIN-5, A LECTIN-LIKE DEFENSE PROTEIN FROM PHASEOLUS VULGARIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris

Hamelryck, T.Poortmans, F.Goossens, A.Angenon, G.Van Montagu, M.Wyns, L.Loris, R.

(1996) J Biol Chem 271: 32796-32802

  • DOI: 10.1074/jbc.271.51.32796
  • Primary Citation of Related Structures:  
    1IOA

  • PubMed Abstract: 
  • In the seeds of the legume plants, a class of sugar-binding proteins with high structural and sequential identity is found, generally called the legume lectins. The seeds of the common bean (Phaseolus vulgaris) contain, besides two such lectins, a lectin-like defense protein called arcelin, in which one sugar binding loop is absent ...

    In the seeds of the legume plants, a class of sugar-binding proteins with high structural and sequential identity is found, generally called the legume lectins. The seeds of the common bean (Phaseolus vulgaris) contain, besides two such lectins, a lectin-like defense protein called arcelin, in which one sugar binding loop is absent. Here we report the crystal structure of arcelin-5 (Arc5), one of the electrophoretic variants of arcelin, solved at a resolution of 2.7 A. The R factor of the refined structure is 20.6%, and the free R factor is 27.1%. The main difference between Arc5 and the legume lectins is the absence of the metal binding loop. The bound metals are necessary for the sugar binding capabilities of the legume lectins and stabilize an Ala-Asp cis-peptide bond. Surprisingly, despite the absence of the metal binding site in Arc5, this cis-peptide bond found in all legume lectin structures is still present, although the Asp residue has been replaced by a Tyr residue. Despite the high identity between the different legume lectin sequences, they show a broad range of quaternary structures. The structures of three different dimers and three different tetramers have been solved. Arc5 crystallized as a monomer, bringing the number of known quaternary structures to seven.


    Related Citations: 
    • The Crystallographic Structure of Phytohemagglutinin-L
      Hamelryck, T.W., Dao-Thi, M.H., Poortmans, F., Chrispeels, M.J., Wyns, L., Loris, R.
      (1996) J Biol Chem 271: 20479
    • Lectins, Lectin Genes, and Their Role in Plant Defense
      Chrispeels, M.J., Raikhel, N.V.
      (1991) Plant Cell 3: 1

    Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 Sint-Genesius-Rode, Belgium. thamelry@vub.ac.be



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ARCELIN-5AA, B240Phaseolus vulgarisMutation(s): 0 
Gene Names: ARC5AARC5-1ARC5-I
UniProt
Find proteins for Q42460 (Phaseolus vulgaris)
Explore Q42460 
Go to UniProtKB:  Q42460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42460
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranoseC, D 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.3α = 90
b = 94.5β = 94.97
c = 82.9γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2014-11-26
    Changes: Other
  • Version 1.4: 2018-04-18
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary