7RAH

Adenylate cyclase toxin RTX domain fragment bound to M1H5 Fab and M2B10 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes.

Goldsmith, J.A.DiVenere, A.M.Maynard, J.A.McLellan, J.S.

(2021) PLoS Pathog 17: e1009920-e1009920

  • DOI: 10.1371/journal.ppat.1009920
  • Primary Citation of Related Structures:  
    7RAH

  • PubMed Abstract: 
  • RTX leukotoxins are a diverse family of prokaryotic virulence factors that are secreted by the type 1 secretion system (T1SS) and target leukocytes to subvert host defenses. T1SS substrates all contain a C-terminal RTX domain that mediates recruitment to the T1SS and drives secretion via a Brownian ratchet mechanism ...

    RTX leukotoxins are a diverse family of prokaryotic virulence factors that are secreted by the type 1 secretion system (T1SS) and target leukocytes to subvert host defenses. T1SS substrates all contain a C-terminal RTX domain that mediates recruitment to the T1SS and drives secretion via a Brownian ratchet mechanism. Neutralizing antibodies against the Bordetella pertussis adenylate cyclase toxin, an RTX leukotoxin essential for B. pertussis colonization, have been shown to target the RTX domain and prevent binding to the αMβ2 integrin receptor. Knowledge of the mechanisms by which antibodies bind and neutralize RTX leukotoxins is required to inform structure-based design of bacterial vaccines, however, no structural data are available for antibody binding to any T1SS substrate. Here, we determine the crystal structure of an engineered RTX domain fragment containing the αMβ2-binding site bound to two neutralizing antibodies. Notably, the receptor-blocking antibodies bind to the linker regions of RTX blocks I-III, suggesting they are key neutralization-sensitive sites within the RTX domain and are likely involved in binding the αMβ2 receptor. As the engineered RTX fragment contained these key epitopes, we assessed its immunogenicity in mice and showed that it elicits similar neutralizing antibody titers to the full RTX domain. The results from these studies will support the development of bacterial vaccines targeting RTX leukotoxins, as well as next-generation B. pertussis vaccines.


    Organizational Affiliation

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
M1H5 Fab Light ChainA215Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
M1H5 Fab Heavy ChainB233Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
M2B10 Fab Light ChainC214Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
M2B10 Fab Heavy ChainD235Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaAE458Bordetella pertussisMutation(s): 0 
Gene Names: cyacyaAFF138_04025NCTC10911_01123
EC: 4.6.1.1
UniProt
Find proteins for P0DKX7 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore P0DKX7 
Go to UniProtKB:  P0DKX7
Entity Groups  
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UniProt GroupP0DKX7
Protein Feature View
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth E],
H [auth E],
I [auth E],
J [auth E],
K [auth E],
G [auth E],
H [auth E],
I [auth E],
J [auth E],
K [auth E],
L [auth E],
M [auth E],
N [auth E],
O [auth E],
P [auth E],
Q [auth E],
R [auth E],
S [auth E],
T [auth E],
U [auth E],
V [auth E],
W [auth E],
X [auth E],
Y [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.559α = 90
b = 117.02β = 90
c = 254.709γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI122753

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Database references