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- EMDB-47483: Cryo EM structure of pertussis toxin in complex with neutralizing... -

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Basic information

Entry
Database: EMDB / ID: EMD-47483
TitleCryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61
Map datastructure of pertussis toxin in complex with neutralizing Fab PERT-61
Sample
  • Complex: pertussis toxin in complex with neutralizing Fab PERT-61
    • Protein or peptide: Pertussis toxin subunit 1
    • Protein or peptide: Pertussis toxin subunit 3
    • Protein or peptide: Pertussis toxin subunit 4
    • Protein or peptide: Pertussis toxin subunit 5
    • Protein or peptide: Islet-activating protein S2
    • Protein or peptide: PERT-61 HC
    • Protein or peptide: PERT-61 LC
KeywordsPTx / mAb / Whooping / TOXIN / TOXIN-Immune System complex
Function / homology
Function and homology information


NAD+ poly-ADP-ribosyltransferase 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 B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / 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 B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / 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
Islet-activating protein S2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4 / Pertussis toxin subunit 1
Similarity search - Component
Biological speciesBordetella pertussis (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBinshtein E / Crowe JE
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61
Authors: Binshtein E / Crowe JE
History
DepositionOct 23, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47483.png

Downloads & links

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Map

FileDownload / File: emd_47483.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of pertussis toxin in complex with neutralizing Fab PERT-61
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 460 pix.
= 297.62 Å		0.65 Å/pix.
x 460 pix.
= 297.62 Å		0.65 Å/pix.
x 460 pix.
= 297.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.8098758 - 2.5897713
Average (Standard dev.)0.00041701307 (±0.04687398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 297.62 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_47483_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47483_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pertussis toxin in complex with neutralizing Fab PERT-61

EntireName: pertussis toxin in complex with neutralizing Fab PERT-61
Components
  • Complex: pertussis toxin in complex with neutralizing Fab PERT-61
    • Protein or peptide: Pertussis toxin subunit 1
    • Protein or peptide: Pertussis toxin subunit 3
    • Protein or peptide: Pertussis toxin subunit 4
    • Protein or peptide: Pertussis toxin subunit 5
    • Protein or peptide: Islet-activating protein S2
    • Protein or peptide: PERT-61 HC
    • Protein or peptide: PERT-61 LC

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Supramolecule #1: pertussis toxin in complex with neutralizing Fab PERT-61

SupramoleculeName: pertussis toxin in complex with neutralizing Fab PERT-61
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bordetella pertussis (bacteria)

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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
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 30.005188 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString: MRCTRAIRQT ARTGWLTWLA ILAVTAPVTS PAWADDPPAT VYRYDSRPPE DVFQNGFTAW GNNDNVLEHL TGRSCQVGSS NSAFVSTSS SRRYTEVYLE HRMQEAVEAE RAGRGTGHFI GYIYEVRADN NFYGAASSYF EYVDTYGDNA GRILAGALAT Y QSEYLAHR ...String:
MRCTRAIRQT ARTGWLTWLA ILAVTAPVTS PAWADDPPAT VYRYDSRPPE DVFQNGFTAW GNNDNVLEHL TGRSCQVGSS NSAFVSTSS SRRYTEVYLE HRMQEAVEAE RAGRGTGHFI GYIYEVRADN NFYGAASSYF EYVDTYGDNA GRILAGALAT Y QSEYLAHR RIPPENIRRV TRVYHNGITG ETTTTEYSNA RYVSQQTRAN PNPYTSRRSV ASIVGTLVRM APVVGACMAR QA ESSEAMA AWSERAGEAM VLVYYESIAY SF

UniProtKB: Pertussis toxin subunit 1

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Macromolecule #2: Pertussis toxin subunit 3

MacromoleculeName: Pertussis toxin subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 25.01282 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString: MLINNKKLLH HILPILVLAL LGMRTAQAVA PGIVIPPKAL FTQQGGAYGR CPNGTRALTV AELRGNAELQ TYLRQITPGW SIYGLYDGT YLGQAYGGII KDAPPGAGFI YRETFCITTI YKTGQPAADH YYSKVTATRL LASTNSRLCA VFVRDGQSVI G ACASPYEG ...String:
MLINNKKLLH HILPILVLAL LGMRTAQAVA PGIVIPPKAL FTQQGGAYGR CPNGTRALTV AELRGNAELQ TYLRQITPGW SIYGLYDGT YLGQAYGGII KDAPPGAGFI YRETFCITTI YKTGQPAADH YYSKVTATRL LASTNSRLCA VFVRDGQSVI G ACASPYEG RYRDMYDALR RLLYMIYMSG LAVRVHVSKE EQYYDYEDAT FQTYALTGIS LCNPAASIC

UniProtKB: Pertussis toxin subunit 3

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Macromolecule #3: Pertussis toxin subunit 4

MacromoleculeName: Pertussis toxin subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 16.566744 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString:
MLRRFPTRTT APGQGGARRS RVRALAWLLA SGAMTHLSPA LADVPYVLVK TNMVVTSVAM KPYEVTPTRM LVCGIAAKLG AAASSPDAH VPFCFGKDLK RPGSSPMEVM LRAVFMQQRP LRMFLGPKQL TFEGKPALEL IRMVECSGKQ DCP

UniProtKB: Pertussis toxin subunit 4

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Macromolecule #4: Pertussis toxin subunit 5

MacromoleculeName: Pertussis toxin subunit 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 14.513755 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString:
MQRQAGLPLK ANPMHTIASI LLSVLGIYSP ADVAGLPTHL YKNFTVQELA LKLKGKNQEF CLTAFMSGRS LVRACLSDAG HEHDTWFDT MLGFAISAYA LKSRIALTVE DSPYPGTPGD LLELQICPLN GYCE

UniProtKB: Pertussis toxin subunit 5

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Macromolecule #5: Islet-activating protein S2

MacromoleculeName: Islet-activating protein S2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bordetella pertussis (bacteria)
Molecular weightTheoretical: 24.856299 KDa
Recombinant expressionOrganism: Bordetella pertussis (bacteria)
SequenceString: MPIDRKTLCH LLSVLPLALL GSHVARASTP GIVIPPQEQI TQHGSPYGRC ANKTRALTVA ELRGSGDLQE YLRHVTRGWS IFALYDGTY LGGEYGGVIK DGTPGGAFDL KTTFCIMTTR NTGQPATDHY YSNVTATRLL SSTNSRLCAV FVRSGQPVIG A CTSPYDGK ...String:
MPIDRKTLCH LLSVLPLALL GSHVARASTP GIVIPPQEQI TQHGSPYGRC ANKTRALTVA ELRGSGDLQE YLRHVTRGWS IFALYDGTY LGGEYGGVIK DGTPGGAFDL KTTFCIMTTR NTGQPATDHY YSNVTATRLL SSTNSRLCAV FVRSGQPVIG A CTSPYDGK YWSMYSRLRK MLYLIYVAGI SVRVHVSKEE QYYDYEDATF ETYALTGISI CNPGSSLC

UniProtKB: Islet-activating protein S2

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Macromolecule #6: PERT-61 HC

MacromoleculeName: PERT-61 HC / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.131942 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QITLKESGPT LVKPTQTLTL TCTFSGFSLS PDIGGVGVGW IRQPPGKALE WLALIYWDDD KRYSPSLQSR LTITKDTSKN RVVLTMINM DPVDTATYYC AHRRPPAYDS SDGDAFDIWG QGTMVTVSS

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Macromolecule #7: PERT-61 LC

MacromoleculeName: PERT-61 LC / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.485893 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPDS LAVSLGERAT INCKSSQSVF SSSNKKNNLA WYQQKPGQPP KLLIYWASTR ESGVPVRFSG SGSGTDFTLT ISSLQAEDV TVYYCQQYYT TPYTFGQGTK LEIK

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4500 / Average electron dose: 56.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326130
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9e3h:
Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61

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