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- PDB-7o85: Anthrax toxin prepore in complex with the neutralizing Fab cAb29 -

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Basic information

Entry
Database: PDB / ID: 7o85
TitleAnthrax toxin prepore in complex with the neutralizing Fab cAb29
Components
  • (Fab) x 2
  • Protective antigen PA-63
KeywordsTOXIN / Anthrax / PA / neutralizing / Fab
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding ...positive regulation of apoptotic process in another organism / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane / metal ion binding
Similarity search - Function
Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 ...Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHoelzgen, F. / Zalk, R. / Alcalay, R. / Cohen-Schwartz, S. / Garau, G. / Shahar, A. / Mazor, O. / Frank, G.A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation364/20 Israel
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Neutralization of the anthrax toxin by antibody-mediated stapling of its membrane-penetrating loop.
Authors: F Hoelzgen / R Zalk / R Alcalay / S Cohen-Schwartz / G Garau / A Shahar / O Mazor / G A Frank /
Abstract: Anthrax infection is associated with severe illness and high mortality. Protective antigen (PA) is the central component of the anthrax toxin, which is one of two major virulence factors of Bacillus ...Anthrax infection is associated with severe illness and high mortality. Protective antigen (PA) is the central component of the anthrax toxin, which is one of two major virulence factors of Bacillus anthracis, the causative agent of anthrax disease. Upon endocytosis, PA opens a pore in the membranes of endosomes, through which the cytotoxic enzymes of the toxin are extruded. The PA pore is formed by a cooperative conformational change in which the membrane-penetrating loops of PA associate, forming a hydrophobic rim that pierces the membrane. Due to its crucial role in anthrax progression, PA is an important target for monoclonal antibody-based therapy. cAb29 is a highly effective neutralizing antibody against PA. Here, the cryo-EM structure of PA in complex with the Fab portion of cAb29 was determined. It was found that cAb29 neutralizes the toxin by clamping the membrane-penetrating loop of PA to the static surface-exposed loop of the D3 domain of the same subunit, thereby preventing pore formation. These results provide the structural basis for the antibody-based neutralization of PA and bring into focus the membrane-penetrating loop of PA as a target for the development of better anti-anthrax vaccines.
#1: Journal: Biorxiv / Year: 2021
Title: Neutralization of the anthrax toxin by antibody-mediated stapling of its membrane penetrating loop
Authors: Hoelzgen, F. / Zalk, R. / Alcalay, R. / Garau, G. / Shahar, A. / Mazor, O. / Frank, G.A.
History
DepositionApr 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / em_admin / pdbx_database_proc
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
A: Protective antigen PA-63
B: Fab
C: Fab
D: Protective antigen PA-63
E: Fab
F: Fab
G: Protective antigen PA-63
H: Fab
I: Fab
J: Protective antigen PA-63
K: Fab
L: Fab
M: Protective antigen PA-63
N: Fab
O: Fab
P: Protective antigen PA-63
Q: Fab
R: Fab
S: Protective antigen PA-63
T: Fab
U: Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)489,54135
Polymers488,98021
Non-polymers56114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area39960 Å2
ΔGint-183 kcal/mol
Surface area176290 Å2
MethodPISA

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Components

#1: Protein
Protective antigen PA-63 / PA63


Mass: 49244.438 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pagA, pag, pXO1-110, BXA0164, GBAA_pXO1_0164 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): V770-NP1-R / References: UniProt: P13423
#2: Antibody
Fab


Mass: 10023.125 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody
Fab


Mass: 10586.680 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Fab bound to anthrax protective antigenCOMPLEX#1-#30MULTIPLE SOURCES
2anthrax protective antigenCOMPLEX#11RECOMBINANT
3FabCOMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.791 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bacillus anthracis (anthrax bacterium)1392
23Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bacillus anthracis (anthrax bacterium)1392
23Cricetulus griseus (Chinese hamster)10029
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 211098 / Symmetry type: POINT

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