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- PDB-9n8i: Pfs230 domain 1 bound by RUPA-39 Fab -

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Basic information

Entry
Database: PDB / ID: 9n8i
TitlePfs230 domain 1 bound by RUPA-39 Fab
Components
  • Anti-kappa nanobody
  • Gametocyte surface protein P230
  • RUPA-39 Heavy chain
  • RUPA-39 Kappa chain
KeywordsIMMUNE SYSTEM / Antibody / Malaria
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 speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsIvanochko, D. / Semesi, A. / Julien, J.P.
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-008866 and OPP1156262 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI148557-01A1 United States
Canadian Institutes of Health Research (CIHR)428410 Canada
CitationJournal: Nat Commun / Year: 2026
Title: A stabilized tandem antigen chimera that elicits potent malaria transmission-reducing activity.
Authors: Danton Ivanochko / Kazutoyo Miura / Sophia Hailemariam / Rashmi Ravichandran / Yiting Song / Wei-Chiao Huang / Rianne Stoter / Karina Teelen / Geert-Jan van Gemert / Elizabeth M Leaf / ...Authors: Danton Ivanochko / Kazutoyo Miura / Sophia Hailemariam / Rashmi Ravichandran / Yiting Song / Wei-Chiao Huang / Rianne Stoter / Karina Teelen / Geert-Jan van Gemert / Elizabeth M Leaf / Sidney Chan / Christine Men / Anthony Semesi / Carol Shiu / Randall S MacGill / Carole A Long / Matthijs M Jore / Neil P King / Jonathan F Lovell / Jean-Philippe Julien /
Abstract: Malaria parasite transmission remains a barrier to elimination since asymptomatic individuals sustain the infectious reservoir. Transmission-blocking vaccine (TBV) candidates targeting Plasmodium ...Malaria parasite transmission remains a barrier to elimination since asymptomatic individuals sustain the infectious reservoir. Transmission-blocking vaccine (TBV) candidates targeting Plasmodium falciparum (Pf) gametocyte surface proteins Pfs230 and Pfs48/45 have shown promise in clinical trials. Several vaccine candidates have been developed for these antigens, yet it is unclear which elicit the most robust and durable transmission-blocking responses. From structure-function relationships of monoclonal antibodies in complex with both antigens, we report the development of a stabilized tandem antigen chimera (STAC), which presents the most potent epitopes from Pfs230 domain 1 (Pfs230-D1) and Pfs48/45 domain 3 (Pfs48/45-D3) in a single construct, while masking non-functional epitopes using an engineered pseudo-native domain disposition. Iterative structure-guided optimization improved antigen yields and stability, while nanoparticle-based multimerization enhanced the functional transmission-reducing activity elicited by the immunogen in female mice. Immunizations with STAC genetically conjugated to self-assembling protein nanoparticles elicited antibodies with potent transmission-reducing activity comparable or superior to the multimerized Pfs230-D1 and Pfs48/45-D3. These findings establish STAC as a promising next-generation TBV candidate to disrupt malaria transmission and accelerate elimination efforts. More broadly, our results support the engineering of highly ordered and stable multi-domain antigens in a single protein as a strategy for the cost-efficient development of multi-component vaccines.
History
DepositionFeb 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUPA-39 Heavy chain
B: RUPA-39 Kappa chain
E: Gametocyte surface protein P230
F: Anti-kappa nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,95515
Polymers81,2944
Non-polymers66111
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.950, 76.110, 88.640
Angle α, β, γ (deg.)90.000, 96.340, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules E

#3: Protein Gametocyte surface protein P230


Mass: 20515.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Homo sapiens (human) / References: UniProt: P68874

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Antibody , 3 types, 3 molecules ABF

#1: Antibody RUPA-39 Heavy chain


Mass: 24054.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody RUPA-39 Kappa chain


Mass: 23420.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Anti-kappa nanobody


Mass: 13303.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 339 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 200 mM Calcium acetate, 20% PEG 3350, 15% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→48.54 Å / Num. obs: 70596 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 35.58 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.071 / Net I/σ(I): 7.8
Reflection shellResolution: 1.85→1.89 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4309 / Rpim(I) all: 0.847

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→48.54 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2332 2000 2.83 %
Rwork0.1884 68553 -
obs0.1896 70553 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5713 0 41 328 6082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00885873
X-RAY DIFFRACTIONf_angle_d1.09227950
X-RAY DIFFRACTIONf_chiral_restr0.0678888
X-RAY DIFFRACTIONf_plane_restr0.011018
X-RAY DIFFRACTIONf_dihedral_angle_d15.22612137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.37631410.35834833X-RAY DIFFRACTION98.61
1.9-1.950.34921410.31224823X-RAY DIFFRACTION98.57
1.95-20.28881410.2954846X-RAY DIFFRACTION98.75
2-2.070.3311410.26674859X-RAY DIFFRACTION99.07
2.07-2.140.26641430.22664873X-RAY DIFFRACTION99.13
2.14-2.230.26441420.21744859X-RAY DIFFRACTION99.09
2.23-2.330.26951430.20764910X-RAY DIFFRACTION99.21
2.33-2.450.25681430.20444896X-RAY DIFFRACTION99.41
2.45-2.610.25151430.20644922X-RAY DIFFRACTION99.69
2.61-2.810.26211430.21294874X-RAY DIFFRACTION99.72
2.81-3.090.22121430.1944929X-RAY DIFFRACTION99.74
3.09-3.540.22971450.18294952X-RAY DIFFRACTION99.8
3.54-4.460.21951450.15654960X-RAY DIFFRACTION99.55
4.46-48.540.1891460.1565017X-RAY DIFFRACTION99.54

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