Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 146.49 kDa 
• Atom Count: 9183 
• Modelled Residue Count: 1182 
• Deposited Residue Count: 1355 
• Unique protein chains: 5

7RAH

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

• PDB DOI: 10.2210/pdb7RAH/pdb

• Classification: IMMUNE SYSTEM/TOXIN
• Organism(s): Mus musculus, Bordetella pertussis
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-01 Released: 2021-09-15 
• Deposition Author(s): Goldsmith, J.A., McLellan, J.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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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 

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

• PubMed: 34547035 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M1H5 Fab Light Chain	A	215	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M1H5 Fab Heavy Chain	B	233	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
M2B10 Fab Light Chain	C	214	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
M2B10 Fab Heavy Chain	D	235	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaA	E	458	Bordetella pertussis	Mutation(s): 0  Gene Names: cya, cyaA, FF138_04025, NCTC10911_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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	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

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 = 65.559	α = 90
b = 117.02	β = 90
c = 254.709	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-07-01 
• Released Date: 2021-09-15 
Deposition Author(s): Goldsmith, J.A., McLellan, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI122753

Revision History  

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