4DWS

Crystal Structure of a chitinase from the Yersinia entomophaga toxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device.

Busby, J.N.Panjikar, S.Landsberg, M.J.Hurst, M.R.Lott, J.S.

(2013) Nature 501: 547-550

  • DOI: 10.1038/nature12465
  • Primary Citation of Related Structures:  4IGL

  • PubMed Abstract: 
  • The ABC toxin complexes produced by certain bacteria are of interest owing to their potent insecticidal activity and potential role in human disease. These complexes comprise at least three proteins (A, B and C), which must assemble to be fully toxic ...

    The ABC toxin complexes produced by certain bacteria are of interest owing to their potent insecticidal activity and potential role in human disease. These complexes comprise at least three proteins (A, B and C), which must assemble to be fully toxic. The carboxy-terminal region of the C protein is the main cytotoxic component, and is poorly conserved between different toxin complexes. A general model of action has been proposed, in which the toxin complex binds to the cell surface via the A protein, is endocytosed, and subsequently forms a pH-triggered channel, allowing the translocation of C into the cytoplasm, where it can cause cytoskeletal disruption in both insect and mammalian cells. Toxin complexes have been visualized using single-particle electron microscopy, but no high-resolution structures of the components are available, and the role of the B protein in the mechanism of toxicity remains unknown. Here we report the three-dimensional structure of the complex formed between the B and C proteins, determined to 2.5 Å by X-ray crystallography. These proteins assemble to form an unprecedented, large hollow structure that encapsulates and sequesters the cytotoxic, C-terminal region of the C protein like the shell of an egg. The shell is decorated on one end by a β-propeller domain, which mediates attachment of the B-C heterodimer to the A protein in the native complex. The structure reveals how C auto-proteolyses when folded in complex with B. The C protein is the first example, to our knowledge, of a structure that contains rearrangement hotspot (RHS) repeats, and illustrates a marked structural architecture that is probably conserved across both this widely distributed bacterial protein family and the related eukaryotic tyrosine-aspartate (YD)-repeat-containing protein family, which includes the teneurins. The structure provides the first clues about the function of these protein repeat families, and suggests a generic mechanism for protein encapsulation and delivery.


    Organizational Affiliation

    AgResearch Structural Biology Laboratory, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chi2
A
546Yersinia entomophagaGene Names: chi2
Find proteins for B6A879 (Yersinia entomophaga)
Go to UniProtKB:  B6A879
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chi2
B
546Yersinia entomophagaGene Names: chi2
Find proteins for B6A879 (Yersinia entomophaga)
Go to UniProtKB:  B6A879
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chi2
C
546Yersinia entomophagaGene Names: chi2
Find proteins for B6A879 (Yersinia entomophaga)
Go to UniProtKB:  B6A879
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Chi2
D
546Yersinia entomophagaGene Names: chi2
Find proteins for B6A879 (Yersinia entomophaga)
Go to UniProtKB:  B6A879
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A, B, C, D
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
MLZ
Query on MLZ
A, B, C, D
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
MLY
Query on MLY
A, B, C, D
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.505α = 90.00
b = 210.556β = 95.27
c = 92.584γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2013-10-09
    Type: Database references