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- EMDB-12761: Anthrax toxin prepore in complex with the neutralizing Fab cAb29 -

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Basic information

Entry
Database: EMDB / ID: EMD-12761
TitleAnthrax toxin prepore in complex with the neutralizing Fab cAb29
Map dataAnthrax toxin prepore in complex with the neutralizing Fab cAb29
Sample
  • Complex: Fab bound to anthrax protective antigen
    • Complex: anthrax protective antigen
      • Protein or peptide: Protective antigen PA-63
    • Complex: Fab
      • Protein or peptide: Fab
      • Protein or peptide: Fab
  • Ligand: CALCIUM ION
KeywordsAnthrax / PA / neutralizing / Fab / TOXIN
Function / homology
Function and homology information


symbiont-mediated suppression of host MAPK cascade / host cell cytosol / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / metal ion binding / identical protein binding / membrane
Similarity search - Function
Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / PA14/GLEYA domain / PA14 domain profile. / 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 ...Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / PA14/GLEYA domain / PA14 domain profile. / 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 domain / PA14 / PA14 domain
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHoelzgen F / Zalk R
Funding support Israel, 1 items
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 GA
History
DepositionApr 14, 2021-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o85
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7o85
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12761.png

Downloads & links

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Map

FileDownload / File: emd_12761.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnthrax toxin prepore in complex with the neutralizing Fab cAb29
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.111714065 - 0.18620475
Average (Standard dev.)0.00009695423 (±0.002405374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ278280246
NX/NY/NZ474891
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1120.1860.000

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Supplemental data

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Sample components

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Entire : Fab bound to anthrax protective antigen

EntireName: Fab bound to anthrax protective antigen
Components
  • Complex: Fab bound to anthrax protective antigen
    • Complex: anthrax protective antigen
      • Protein or peptide: Protective antigen PA-63
    • Complex: Fab
      • Protein or peptide: Fab
      • Protein or peptide: Fab
  • Ligand: CALCIUM ION

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Supramolecule #1: Fab bound to anthrax protective antigen

SupramoleculeName: Fab bound to anthrax protective antigen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 791 KDa

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Supramolecule #2: anthrax protective antigen

SupramoleculeName: anthrax protective antigen / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)

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Supramolecule #3: Fab

SupramoleculeName: Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Protective antigen PA-63

MacromoleculeName: Protective antigen PA-63 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 49.244438 KDa
Recombinant expressionOrganism: Bacillus anthracis (anthrax bacterium)
SequenceString: TVPDRDNDGI PDSLEVEGYT VDVKNKRTFL SPWISNIHEK KGLTKYKSSP EKWSTASDPY SDFEKVTGRI DKNVSPEARH PLVAAYPIV HVDMENIILS KNEDQSTQNT DSQTRTISKN TSTSRTHTSE VHGNAEVHAS FFDIGGSVSA GFSNSNSSTV A IDHSLSLA ...String:
TVPDRDNDGI PDSLEVEGYT VDVKNKRTFL SPWISNIHEK KGLTKYKSSP EKWSTASDPY SDFEKVTGRI DKNVSPEARH PLVAAYPIV HVDMENIILS KNEDQSTQNT DSQTRTISKN TSTSRTHTSE VHGNAEVHAS FFDIGGSVSA GFSNSNSSTV A IDHSLSLA GERTWAETMG LNTADTARLN ANIRYVNTGT APIYNVLPTT SLVLGKNQTL ATIKAKENQL SQILAPNNYY PS KNLAPIA LNAQDDFSST PITMNYNQFL ELEKTKQLRL DTDQVYGNIA TYNFENGRVR VDTGSNWSEV LPQIQETTAR IIF NGKDLN LVERRIAAVN PSDPLETTKP DMTLKEALKI AFGFNEPNGN LQYQGKDITE FDFNFDQQTS QNIKNQLAEL NATN IYTVL DKIKLNAKMN ILIRDKRFHY DRNNIAVGAD ESVVKE

UniProtKB: Protective antigen

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Macromolecule #2: Fab

MacromoleculeName: Fab / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.023125 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
AAAAAAAAAA AAAAAAAAAA ISCRASQDIS NYLNWYAAAA AAAAALLIYY TSRLHSEVPS RFSGSGSGTD YSLTIAAAAA AAAAAAFCQ QGKTLPWTFG GGTKL

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Macromolecule #3: Fab

MacromoleculeName: Fab / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.58668 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAKASGYIFT NYNMHWVAAA AAAAAEWIGA IYPRTGDTSY NQKFKGKATL TADKSSSTAY AAAAAAAAA AAAAAACARD GFAYWAAAAA AAAA

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211098
Initial angle assignmentType: OTHER / Details: Stochastic Gradient descent
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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