5G37

MR structure of the binary mosquito larvicide BinAB at pH 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

De Novo Phasing with X-Ray Laser Reveals Mosquito Larvicide Binab Structure.

Colletier, J.Sawaya, M.R.Gingery, M.Rodriguez, J.A.Cascio, D.Brewster, A.S.Michels-Clark, T.Hice, R.H.Coquelle, N.Boutet, S.Williams, G.J.Messerschmidt, M.Deponte, D.P.Sierra, R.G.Laksmono, H.Koglin, J.E.Hunter, M.S.Park, H.Uervirojnangkoorn, M.Bideshi, D.K.Brunger, A.T.Federici, B.A.Sauter, N.K.Eisenberg, D.S.

(2016) Nature 539: 43

  • DOI: 10.1038/nature19825
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step int ...

    BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals-50 unit cells per edge, on average-has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure reveals tyrosine- and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.


    Organizational Affiliation

    UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA.,Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Biological Sciences, California Baptist University, Riverside, California 92504, USA.,Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1570, USA.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
41.9 KDA INSECTICIDAL TOXIN
A
366Lysinibacillus sphaericusMutation(s): 0 
Gene Names: binA
Find proteins for P06575 (Lysinibacillus sphaericus)
Go to UniProtKB:  P06575
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LARVICIDAL TOXIN 51 KDA PROTEIN
B
448Lysinibacillus sphaericusMutation(s): 0 
Gene Names: binB (sph04)
Find proteins for P10565 (Lysinibacillus sphaericus)
Go to UniProtKB:  P10565
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.787α = 90.00
b = 96.996β = 90.00
c = 127.075γ = 90.00
Software Package:
Software NamePurpose
cctbx.xfeldata reduction
PHASERphasing
PHENIXrefinement
cctbx.primedata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references
  • Version 1.2: 2016-11-09
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Data collection
  • Version 1.4: 2018-11-14
    Type: Data collection
  • Version 1.5: 2019-08-28
    Type: Data collection