5FOZ

De novo structure of the binary mosquito larvicide BinAB at pH 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.6 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: https://doi.org/10.1038/nature19825
  • Primary Citation of Related Structures:  
    5FOY, 5FOZ, 5G37

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TOXIN370Lysinibacillus sphaericusMutation(s): 0 
UniProt
Find proteins for P06575 (Lysinibacillus sphaericus)
Explore P06575 
Go to UniProtKB:  P06575
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06575
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LARVICIDAL TOXIN PROTEIN448Lysinibacillus sphaericusMutation(s): 0 
UniProt
Find proteins for P10565 (Lysinibacillus sphaericus)
Explore P10565 
Go to UniProtKB:  P10565
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10565
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.67α = 90
b = 97.286β = 90
c = 127.654γ = 90
Software Package:
Software NamePurpose
cctbx.xfeldata reduction
cctbx.primedata scaling
SHELXDphasing
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2016-11-09
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Data collection
  • Version 1.4: 2018-11-14
    Changes: Data collection
  • Version 1.5: 2019-08-28
    Changes: Data collection
  • Version 1.6: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description