1RF2 Toxin date Nov 07, 2003
title Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand Bv4
authors J.C.Pickens, D.D.Mitchell, J.Liu, X.Tan, Z.Zhang, C.L.Verlinde, W.G.Hol, E.Fan
compound source
Molecule: Cholera Toxin B Protein (Ctb)
Chain: D, E, F, G, H
Engineered: Yes
 Organism_scientific: Vibrio Cholerae
Organism_common: Bacteria
Gene: Ctxb
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_strain: Top10
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbad
symmetry Space Group: C 1 2 1
R_factor 0.132
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.235 66.028 78.642 90.00 105.80 90.00
method X-Ray Diffractionresolution 1.35 Å
ligand BV4, PGE, TMN enzyme
similarity Belongs to the Enterotoxin_b family.
subunit The a subunit contains two chains, a1 and a2, linked by a disulfide bridge. The holotoxin (choleragen) consists of a pentameric ring of b subunits whose central pore is occupied by the a subunit.
gene ctxB (V. cholerae)
function It can bind five gm1 gangliosides. The b subunit pentameric ring directs the a subunit to its target by binding to the gm1 gangliosides present on the surface of the intestinal epithelial cells. It has no toxic activity by itself.
Gene
Ontology
ChainFunctionProcessComponent
H, F, D, G, E
  • pathogenesis
  • extracellular region
  • membrane
    • Primary referenceNonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer., Pickens JC, Mitchell DD, Liu J, Tan X, Zhang Z, Verlinde CL, Hol WG, Fan E, Chem Biol 2004 Sep;11(9):1205-15. PMID:15380181
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (216 Kb) [Save to disk]
  • Biological Unit Coordinates (1rf2.pdb1.gz) 190 Kb
  • CSU: Contacts of Structural Units for 1RF2
  • Likely Quarternary Molecular Structure file(s) for 1RF2
  • Structure Factors (1074 Kb)
  • Retrieve 1RF2 in mmCIF format [Save to disk]
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  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
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    • Structure-derived information
  • Conformational Epitope Prediction for 1RF2 1RF2D 1RF2E 1RF2F 1RF2G 1RF2H from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
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  • 3D motif for 1RF2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rf2d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1rf2e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1rf2f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1e1rf2, region F:9-81 [Jmol] [rasmolscript] [script source]
        - Domain d1rf2g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1rf2h_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1rf2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rf2_F] [1rf2_H] [1rf2_D] [1rf2_E] [1rf2_G]
    • Other resources with information on 1RF2
  • InterPro: IPR001835
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