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- PDB-9n5o: Endogenous Pfs230D7-8 in complex with 18F25 -

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Basic information

Entry
Database: PDB / ID: 9n5o
TitleEndogenous Pfs230D7-8 in complex with 18F25
Components
  • 18F25 Heavy Chain
  • 18F25 Kappa Chain
  • Gametocyte surface protein P230
KeywordsIMMUNE SYSTEM / 6-Cys / antibody
Function / homology: / 6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesMus musculus (house mouse)
Plasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsJackman, J.J. / Yoo, R. / Ivanochko, D. / Hailemariam, S. / Bekkering, E. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: bioRxiv / Year: 2025
Title: Structure of endogenous Pfs230:Pfs48/45 in complex with potent malaria transmission-blocking antibodies.
Authors: Ezra T Bekkering / Randy Yoo / Sophia Hailemariam / Fabian Heide / Danton Ivanochko / Matthew Jackman / Nicholas I Proellochs / Rianne Stoter / Geert-Jan van Gemert / Ayana Maeda / Takaaki ...Authors: Ezra T Bekkering / Randy Yoo / Sophia Hailemariam / Fabian Heide / Danton Ivanochko / Matthew Jackman / Nicholas I Proellochs / Rianne Stoter / Geert-Jan van Gemert / Ayana Maeda / Takaaki Yuguchi / Oscar T Wanders / Renate C van Daalen / Maartje R Inklaar / Carolina M Andrade / Pascal W T C Jansen / Michiel Vermeulen / Teun Bousema / Eizo Takashima / John L Rubinstein / Taco W A Kooij / Matthijs M Jore / Jean-Philippe Julien /
Abstract: The Pfs230:Pfs48/45 complex forms the basis for leading malaria transmission-blocking vaccine candidates, yet little is known about its molecular assembly. Here, we used cryogenic electron microscopy ...The Pfs230:Pfs48/45 complex forms the basis for leading malaria transmission-blocking vaccine candidates, yet little is known about its molecular assembly. Here, we used cryogenic electron microscopy to elucidate the structure of the endogenous Pfs230:Pfs48/45 complex bound to six potent transmission-blocking antibodies. Pfs230 consists of multiple domain clusters rigidified by interactions mediated through insertion domains. Membrane-anchored Pfs48/45 forms a disc-like structure and interacts with a short C-terminal peptide on Pfs230 that is critical for Pfs230 membrane-retention . Interestingly, membrane retention through this interaction is not essential for transmission to mosquitoes, suggesting that complex disruption is not a mode of action for transmission-blocking antibodies. Analyses of Pfs48/45- and Pfs230-targeted antibodies identify conserved epitopes on the Pfs230:Pfs48/45 complex and provides a structural paradigm for complement-dependent activity of Pfs230-targeting antibodies. Altogether, the antibody-bound Pfs230:Pfs48/45 structure presented improves our molecular understanding of this biological complex, informing the development of next-generation transmission-blocking interventions.
History
DepositionFeb 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Gametocyte surface protein P230
H: 18F25 Heavy Chain
L: 18F25 Kappa Chain


Theoretical massNumber of molelcules
Total (without water)410,7353
Polymers410,7353
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Gametocyte surface protein P230


Mass: 363701.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P68874
#2: Antibody 18F25 Heavy Chain


Mass: 23503.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody 18F25 Kappa Chain


Mass: 23530.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
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

ComponentName: Endogenous Pfs230D7-8 in complex with 18F25 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMpotassium chlorideKCl1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K
Details: The Leica Automatic Plunge Freezer EM GP2 was used for freezing.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.5 sec. / Electron dose: 52 e/Å2 / Film or detector model: OTHER
Details: The Falcon 4i Direct Electron Detector was used. Images were collected at average electron doses per image of 50 and 53.7 during two data collections.
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.6.0particle selection
2EPUimage acquisition
4cryoSPARCv4.6.0CTF correction
7UCSF ChimeraX1.9model fitting
12cryoSPARCv4.6.03D reconstruction
19PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137749 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDDetailsSource nameTypeAccession code
11model generated in-houseAlphaFoldin silico model
29N6U

9n6u

1PDBexperimental model9N6U
RefinementHighest resolution: 4.32 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0084529
ELECTRON MICROSCOPYf_angle_d1.1136123
ELECTRON MICROSCOPYf_dihedral_angle_d10.7491684
ELECTRON MICROSCOPYf_chiral_restr0.055673
ELECTRON MICROSCOPYf_plane_restr0.007788

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