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- PDB-9n5i: Endogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pf... -

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Basic information

Entry
Database: PDB / ID: 9n5i
TitleEndogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Components
  • (Gametocyte surface protein ...) x 2
  • RUPA-44 Fab heavy chain
  • RUPA-44 Fab kappa chain
  • RUPA-71 Fab heavy chain
  • RUPA-71 Fab kappa chain
KeywordsIMMUNE SYSTEM / Pfs48/45 / Pfs230 / Malaria / transmission-blocking antibodies
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane
Similarity search - Function
: / 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
Similarity search - Domain/homology
Gametocyte surface protein P230 / Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsHailemariam, S. / Heide, F. / Bekkering, E. / Ivanochko, D. / Yoo, R. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Immunity / Year: 2025
Title: Cryo-EM structure of endogenous Pfs230:Pfs48/45 complex with six antibodies reveals mechanisms of malaria transmission-blocking activity.
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 cryo-electron microscopy to ...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 cryo-electron microscopy to elucidate the structure of the endogenous Pfs230:Pfs48/45 complex bound to six transmission-blocking antibodies. Our structure revealed that Pfs230 consists of multiple domain clusters rigidified by interactions mediated through insertion domains. Membrane-anchored Pfs48/45 formed a disk-like structure, interacting with a short C-terminal peptide on Pfs230 that was critical for Pfs230 membrane-retention in vivo. Membrane retention through this interaction was 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 identified conserved epitopes on the Pfs230:Pfs48/45 complex and provided a structural paradigm for complement-dependent activity of Pfs230-targeting antibodies. Altogether, the antibody-bound Pfs230:Pfs48/45 structure improves our molecular understanding of this biological complex, informing the development of next-generation Plasmodium falciparum transmission-blocking interventions.
History
DepositionFeb 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.2Nov 26, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P230
D: Gametocyte surface protein P45/48
E: RUPA-44 Fab kappa chain
F: RUPA-44 Fab heavy chain
H: RUPA-71 Fab heavy chain
L: RUPA-71 Fab kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,6857
Polymers511,3186
Non-polymers3671
Water00
1


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

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Components

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Gametocyte surface protein ... , 2 types, 2 molecules AD

#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 (malaria parasite P. falciparum)
References: UniProt: P68874
#2: Protein Gametocyte surface protein P45/48


Mass: 51545.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8I6T1

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Antibody , 4 types, 4 molecules EFHL

#3: Antibody RUPA-44 Fab kappa chain


Mass: 23483.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 F / Production host: Homo sapiens (human)
#4: Antibody RUPA-44 Fab heavy chain


Mass: 24277.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 F / Production host: Homo sapiens (human)
#5: Antibody RUPA-71 Fab heavy chain


Mass: 24711.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#6: Antibody RUPA-71 Fab kappa chain


Mass: 23598.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#7: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Details

Has ligand of interestY
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 Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic 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: TFS FALCON 4i (4k x 4k)
Details: Images were collected at average electron doses per image of 50 and 53.7 electrons per square Angstrom 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
9cryoSPARCv4.6.0initial Euler assignment
10cryoSPARCv4.6.0final Euler assignment
11cryoSPARCv4.6.0classification
12cryoSPARCv4.6.03D reconstruction
13PHENIX1.21.1_5286model refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146814 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18U1P

8u1p

18U1P1PDBexperimental model
27UXL

7uxl

17UXL2PDBexperimental model
39N7K

9n7k

19N7K3PDBexperimental model
41AlphaFoldin silico model
RefinementHighest resolution: 3.39 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039451
ELECTRON MICROSCOPYf_angle_d0.52912816
ELECTRON MICROSCOPYf_dihedral_angle_d4.8831292
ELECTRON MICROSCOPYf_chiral_restr0.0461418
ELECTRON MICROSCOPYf_plane_restr0.0041627

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