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- EMDB-80292: Structure of the anthrax protective antigen in complex with a pot... -

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Basic information

Entry
Database: EMDB / ID: EMD-80292
TitleStructure of the anthrax protective antigen in complex with a potent neutralizing antibody
Map data
Sample
  • Complex: Structure of the anthrax protective antigen in complex with a potent neutralizing antibody
    • Protein or peptide: Protective antigen PA-63
    • Protein or peptide: 22F1 VH
    • Protein or peptide: 22F1 VL
Keywordstoxin / antibody / complex / neutralization / ANTITOXIN
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
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) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsFan PF / Yu CM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the anthrax protective antigen in complex with a potent neutralizing antibody
Authors: Fan PF / Yu CM
History
DepositionApr 14, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80292.png

Downloads & links

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Map

FileDownload / File: emd_80292.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 360 pix.
= 270. Å		0.75 Å/pix.
x 360 pix.
= 270. Å		0.75 Å/pix.
x 360 pix.
= 270. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.9536002 - 5.688132
Average (Standard dev.)0.00033611592 (±0.09243235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80292_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80292_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the anthrax protective antigen in complex with a pot...

EntireName: Structure of the anthrax protective antigen in complex with a potent neutralizing antibody
Components
  • Complex: Structure of the anthrax protective antigen in complex with a potent neutralizing antibody
    • Protein or peptide: Protective antigen PA-63
    • Protein or peptide: 22F1 VH
    • Protein or peptide: 22F1 VL

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Supramolecule #1: Structure of the anthrax protective antigen in complex with a pot...

SupramoleculeName: Structure of the anthrax protective antigen in complex with a potent neutralizing antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)

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Macromolecule #1: Protective antigen PA-63

MacromoleculeName: Protective antigen PA-63 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 47.546594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AGPTVPDRDN DGIPDSLEVE GYTVDVKNKR TSLSPWISNI HEKKGLTKYK SSPEKWSTAS DPYSDFEKVT GRIDKNVSPE ARHPLVAAY PIVHVDMENI ILSKNEDQST QNTDSQTRTI SKNTSTSRTH TSEVHGNAEV HASFFDIGGS VSAGFSNSNS S TVAIDHSL ...String:
AGPTVPDRDN DGIPDSLEVE GYTVDVKNKR TSLSPWISNI HEKKGLTKYK SSPEKWSTAS DPYSDFEKVT GRIDKNVSPE ARHPLVAAY PIVHVDMENI ILSKNEDQST QNTDSQTRTI SKNTSTSRTH TSEVHGNAEV HASFFDIGGS VSAGFSNSNS S TVAIDHSL SLAGERTWAE TMGLNTADTA RLNANIRYVN TGTAPIYNVL PTTSLVLGKN QTLATIKAKE NQLSQILAPN NY YPSKNLA PIALNAQDDF SSTPITMNYN QFLELEKTKQ LRLDTDQVYG NIATYNFENG RVRVDTGSNW SEVLPQIQET TAR IIFNGK DLNLVERRIA AVNPSDPLET TKPDMTLKEA LKIAFGFNEP NGNLQYQGKD ITEFDFNFDQ QTSQNIKNQL AELN ATNIY TVLDKIKLNA KMNILIRDKR FH

UniProtKB: Protective antigen

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Macromolecule #2: 22F1 VH

MacromoleculeName: 22F1 VH / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.284215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSQTLSL TCTVSGGSLS SGGSYWSWIR QHPGKGLEYL GYIFYFGRPY YNPSLQSRIT ISVDTSKNQF SLKLNSVTA ADTAVYYCAR ASLRGILWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
QVQLQESGPG LVKPSQTLSL TCTVSGGSLS SGGSYWSWIR QHPGKGLEYL GYIFYFGRPY YNPSLQSRIT ISVDTSKNQF SLKLNSVTA ADTAVYYCAR ASLRGILWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC

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Macromolecule #3: 22F1 VL

MacromoleculeName: 22F1 VL / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.363949 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLSPGERAT LSCRASQSVG NYLAWYQQKL GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSNWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPAT LSLSPGERAT LSCRASQSVG NYLAWYQQKL GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSNWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.04 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: predicted by ModelSmart
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 121316
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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