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- EMDB-48554: Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab... -

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Basic information

Entry
Database: EMDB / ID: EMD-48554
TitleGenetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab
Map dataReconsctruction of pertussis toxin bound to hu1B7 and hu11E6
Sample
  • Complex: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
    • Protein or peptide: Pertussis toxin subunit 1
    • Protein or peptide: Pertussis toxin subunit 2
    • Protein or peptide: Pertussis toxin subunit 3
    • Protein or peptide: Pertussis toxin subunit 4
    • Protein or peptide: Pertussis toxin subunit 5
    • Protein or peptide: hu1B7 Fab light chain
    • Protein or peptide: hu1B7 Fab heavy chain
    • Protein or peptide: hu11E6 Fab light chain
    • Protein or peptide: hu11E6 Fab heavy chain
KeywordsToxin / Pertussis / Antibody
Function / homology
Function and homology information


NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Aerolysin/Pertussis toxin domain ...Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / Enterotoxin / C-type lectin fold
Similarity search - Domain/homology
Pertussis toxin subunit 1 / Pertussis toxin subunit 2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Bordetella pertussis (bacteria) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsGoldsmith JA / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155453 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for neutralizing antibody binding to pertussis toxin.
Authors: Jory A Goldsmith / Annalee W Nguyen / Rebecca E Wilen / Wassana Wijagkanalan / Jason S McLellan / Jennifer A Maynard /
Abstract: Pertussis toxin (PT) is a key protective antigen in vaccine- and natural immunity-mediated protection from infection. Despite its importance, no PT-neutralizing epitopes have been characterized ...Pertussis toxin (PT) is a key protective antigen in vaccine- and natural immunity-mediated protection from infection. Despite its importance, no PT-neutralizing epitopes have been characterized structurally. To define neutralizing epitopes and identify key structural elements to preserve during PT antigen design, we determined a 3.6 Å cryoelectron microscopy structure of genetically detoxified PT (PTg) bound to hu11E6 and hu1B7, two potently neutralizing anti-PT antibodies with complementary mechanisms: disruption of toxin adhesion to cells and intracellular activities, respectively. Hu11E6 binds the paralogous S2 and S3 subunits of PTg via a conserved epitope but surprisingly did not span the previously identified sialic acid-binding site implicated in toxin adhesion. Hu11E6 specifically prevented PTg binding to sialylated N-glycans and a sialylated model receptor, as demonstrated by high-throughput glycan array analysis and ELISA, while a T cell activation assay showed that it blocks PTg mitogenic activities to define its neutralizing mechanism. Hu1B7 bound a quaternary epitope spanning the S1 and S5 subunits, although functional studies of hu1B7 variants suggested that S5 binding is not involved in its PT neutralization mechanism. These results structurally define neutralizing epitopes on PT, improving our molecular understanding of immune protection from and providing key information for the future development of PT immunogens.
History
DepositionJan 7, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48554.png

Downloads & links

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Map

FileDownload / File: emd_48554.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconsctruction of pertussis toxin bound to hu1B7 and hu11E6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 350 pix.
= 385. Å		1.1 Å/pix.
x 350 pix.
= 385. Å		1.1 Å/pix.
x 350 pix.
= 385. 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: 0.644
Minimum - Maximum-0.21250474 - 1.4145198
Average (Standard dev.)-0.00030964022 (±0.041326873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 385.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map for reconstruction of pertussis toxin bound...

Fileemd_48554_additional_1.map
AnnotationSharpened map for reconstruction of pertussis toxin bound to hu1B7 and hu11E6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B for reconstruction of pertussis toxin bound...

Fileemd_48554_half_map_1.map
AnnotationHalf-map B for reconstruction of pertussis toxin bound to hu1B7 and hu11E6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A for reconstruction of pertussis toxin bound...

Fileemd_48554_half_map_2.map
AnnotationHalf-map A for reconstruction of pertussis toxin bound to hu1B7 and hu11E6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of integrin alphaM/beta2 ectodomain with adenylat...

EntireName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
Components
  • Complex: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
    • Protein or peptide: Pertussis toxin subunit 1
    • Protein or peptide: Pertussis toxin subunit 2
    • Protein or peptide: Pertussis toxin subunit 3
    • Protein or peptide: Pertussis toxin subunit 4
    • Protein or peptide: Pertussis toxin subunit 5
    • Protein or peptide: hu1B7 Fab light chain
    • Protein or peptide: hu1B7 Fab heavy chain
    • Protein or peptide: hu11E6 Fab light chain
    • Protein or peptide: hu11E6 Fab heavy chain

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Supramolecule #1: Ternary complex of integrin alphaM/beta2 ectodomain with adenylat...

SupramoleculeName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pertussis toxin subunit 1

MacromoleculeName: Pertussis toxin subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Pentosyltransferases
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 26.148666 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString: DDPPATVYKY DSRPPEDVFQ NGFTAWGNND NVLDHLTGRS CQVGSSNSAF VSTSSSRRYT EVYLEHRMQE AVEAERAGRG TGHFIGYIY EVRADNNFYG AASSYFEYVD TYGDNAGRIL AGALATYQSG YLAHRRIPPE NIRRVTRVYH NGITGETTTT E YSNARYVS ...String:
DDPPATVYKY DSRPPEDVFQ NGFTAWGNND NVLDHLTGRS CQVGSSNSAF VSTSSSRRYT EVYLEHRMQE AVEAERAGRG TGHFIGYIY EVRADNNFYG AASSYFEYVD TYGDNAGRIL AGALATYQSG YLAHRRIPPE NIRRVTRVYH NGITGETTTT E YSNARYVS QQTRANPNPY TSRRSVASIV GTLVRMAPVI GACMARQAES SEAMAAWSER AGEAMVLVYY ESIAYSF

UniProtKB: Pertussis toxin subunit 1

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Macromolecule #2: Pertussis toxin subunit 2

MacromoleculeName: Pertussis toxin subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 21.913676 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString: STPGIVIPPQ EQITQHGGPY GRCANKTRAL TVAELRGSGD LQEYLRHVTR GWSIFALYDG TYLGGEYGGV IKDGTPGGAF DLKTTFCIM TTRNTGQPAT DHYYSNVTAT RLLSSTNSRL CAVFVRSGQP VIGACTSPYD GKYWSMYSRL RKMLYLIYVA G ISVRVHVS ...String:
STPGIVIPPQ EQITQHGGPY GRCANKTRAL TVAELRGSGD LQEYLRHVTR GWSIFALYDG TYLGGEYGGV IKDGTPGGAF DLKTTFCIM TTRNTGQPAT DHYYSNVTAT RLLSSTNSRL CAVFVRSGQP VIGACTSPYD GKYWSMYSRL RKMLYLIYVA G ISVRVHVS KEEQYYDYED ATFETYALTG ISICNPGSSL C

UniProtKB: Pertussis toxin subunit 2

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Macromolecule #3: Pertussis toxin subunit 3

MacromoleculeName: Pertussis toxin subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 21.889867 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString: VAPGIVIPPK ALFTQQGGAY GRCPNGTRAL TVAELRGNAE LQTYLRQITP GWSIYGLYDG TYLGQAYGGI IKDAPPGAGF IYRETFCIT TIYKTGQPAA DHYYSKVTAT RLLASTNSRL CAVFVRDGQS VIGACASPYE GRYRDMYDAL RRLLYMIYMS G LAVRVHVS ...String:
VAPGIVIPPK ALFTQQGGAY GRCPNGTRAL TVAELRGNAE LQTYLRQITP GWSIYGLYDG TYLGQAYGGI IKDAPPGAGF IYRETFCIT TIYKTGQPAA DHYYSKVTAT RLLASTNSRL CAVFVRDGQS VIGACASPYE GRYRDMYDAL RRLLYMIYMS G LAVRVHVS KEEQYYDYED ATFQTYALTG ISLCNPAASI C

UniProtKB: Pertussis toxin subunit 3

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Macromolecule #4: Pertussis toxin subunit 4

MacromoleculeName: Pertussis toxin subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 12.072426 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString:
DVPYVLVKTN MVVTSVAMKP YEVTPTRMLV CGIAAKLGAA ASSPDAHVPF CFGKDLKRPG SSPMEVMLRA VFMQQRPLRM FLGPKQLTF EGKPALELIR MVECSGKQDC P

UniProtKB: Pertussis toxin subunit 4

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Macromolecule #5: Pertussis toxin subunit 5

MacromoleculeName: Pertussis toxin subunit 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 10.951524 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString:
GLPTHLYKNF TVQELALKLK GKNQEFCLTA FMSGRSLVRA CLSDAGHEHD TWFDTMLGFA ISAYALKSRI ALTVEDSPYP GTPGDLLEL QICPLNGYCE

UniProtKB: Pertussis toxin subunit 5

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Macromolecule #6: hu1B7 Fab light chain

MacromoleculeName: hu1B7 Fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.137705 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIVLTQSPAT LSVSPGERVT LTCSASSSVS FMYWYQQKPG RAPKPLIYLT SNLPSGVPAR FSGSGSGTSY TLTINSLEAE DAATYYCQQ WSSHPPTFGS GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
QIVLTQSPAT LSVSPGERVT LTCSASSSVS FMYWYQQKPG RAPKPLIYLT SNLPSGVPAR FSGSGSGTSY TLTINSLEAE DAATYYCQQ WSSHPPTFGS GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #7: hu1B7 Fab heavy chain

MacromoleculeName: hu1B7 Fab heavy chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.868709 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYKFT SYWMHWVRQA PGQGLEWIGN IFPGSGSTNY AQKFQGRVTL TVDTSTSTAY MELSSLRSE DTAVYYCTRW LSGAYFDYWG QGTTVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYKFT SYWMHWVRQA PGQGLEWIGN IFPGSGSTNY AQKFQGRVTL TVDTSTSTAY MELSSLRSE DTAVYYCTRW LSGAYFDYWG QGTTVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDK

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Macromolecule #8: hu11E6 Fab light chain

MacromoleculeName: hu11E6 Fab light chain / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.421963 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPSS LSASVGDRVT ISCRASQDID NYLSWFQQKP GGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YTLTISSLQP EDIATYFCQ QGNTFPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIVMTQSPSS LSASVGDRVT ISCRASQDID NYLSWFQQKP GGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YTLTISSLQP EDIATYFCQ QGNTFPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #9: hu11E6 Fab heavy chain

MacromoleculeName: hu11E6 Fab heavy chain / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.733768 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQVVESGGG LVQPGRSLRL SCTTSGFTFT DYYVSWVRQA PGKALEWLGF IRNKVNGYTT EFSSSVKGRF TISRDNSKSI LYLQMNSLK IEDTAVYYCA RVSYYGRGWY FDYWGQGTTL TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EVQVVESGGG LVQPGRSLRL SCTTSGFTFT DYYVSWVRQA PGKALEWLGF IRNKVNGYTT EFSSSVKGRF TISRDNSKSI LYLQMNSLK IEDTAVYYCA RVSYYGRGWY FDYWGQGTTL TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3k6s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 316937
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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