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- PDB-9n89: Crystal structure of 2A2 malarial antibody -

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Basic information

Entry
Database: PDB / ID: 9n89
TitleCrystal structure of 2A2 malarial antibody
Components
  • 2A2 Heavy Chain
  • 2A2 Kappa Chain
KeywordsIMMUNE SYSTEM / antibody / malaria
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsYoo, 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 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 2A2 Heavy Chain
L: 2A2 Kappa Chain


Theoretical massNumber of molelcules
Total (without water)47,1122
Polymers47,1122
Non-polymers00
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-21 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.974, 76.682, 91.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody 2A2 Heavy Chain


Mass: 23507.283 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)
#2: Antibody 2A2 Kappa Chain


Mass: 23604.301 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG 4K

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920194 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920194 Å / Relative weight: 1
ReflectionResolution: 1.2→28.51 Å / Num. obs: 131804 / % possible obs: 99.52 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.88 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.88
Reflection shellResolution: 1.2→1.21 Å / Num. unique obs: 8275 / CC1/2: 0.716

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→28.51 Å / SU ML: 0.0985 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1941 6511 4.94 %
Rwork0.186 125284 -
obs0.1864 131795 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.84 Å2
Refinement stepCycle: LAST / Resolution: 1.2→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 0 365 3603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00433438
X-RAY DIFFRACTIONf_angle_d0.79754728
X-RAY DIFFRACTIONf_chiral_restr0.0825545
X-RAY DIFFRACTIONf_plane_restr0.0055618
X-RAY DIFFRACTIONf_dihedral_angle_d12.24091257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.25872150.22414031X-RAY DIFFRACTION98.2
1.21-1.230.2312220.2274109X-RAY DIFFRACTION98.86
1.23-1.240.2382040.2244091X-RAY DIFFRACTION98.58
1.24-1.260.23532180.21834135X-RAY DIFFRACTION98.64
1.26-1.280.23982140.21374112X-RAY DIFFRACTION98.95
1.28-1.290.22382240.214090X-RAY DIFFRACTION99.31
1.29-1.310.22881970.20814142X-RAY DIFFRACTION99.09
1.31-1.330.22792070.20714125X-RAY DIFFRACTION99.15
1.33-1.350.20292470.19894107X-RAY DIFFRACTION99.23
1.35-1.370.21152150.20134145X-RAY DIFFRACTION99.34
1.37-1.40.21442320.19874108X-RAY DIFFRACTION99.38
1.4-1.420.20772150.19194175X-RAY DIFFRACTION99.52
1.42-1.450.19322120.19494117X-RAY DIFFRACTION99.61
1.45-1.480.21762160.19274159X-RAY DIFFRACTION99.66
1.48-1.510.19982020.1874166X-RAY DIFFRACTION99.68
1.51-1.550.18252040.18444162X-RAY DIFFRACTION99.7
1.55-1.590.18752190.1774180X-RAY DIFFRACTION99.89
1.59-1.630.19322100.17754199X-RAY DIFFRACTION99.86
1.63-1.680.18982170.17834190X-RAY DIFFRACTION99.91
1.68-1.730.17752210.1864175X-RAY DIFFRACTION99.98
1.73-1.790.20012060.18144189X-RAY DIFFRACTION99.93
1.79-1.870.20371940.17874231X-RAY DIFFRACTION99.95
1.87-1.950.17112340.17734194X-RAY DIFFRACTION99.93
1.95-2.050.17792170.17054197X-RAY DIFFRACTION99.86
2.05-2.180.17682210.17224224X-RAY DIFFRACTION99.89
2.18-2.350.17772190.17544228X-RAY DIFFRACTION99.75
2.35-2.590.22922120.19094244X-RAY DIFFRACTION99.87
2.59-2.960.2022170.19894293X-RAY DIFFRACTION99.89
2.96-3.730.18572300.18664298X-RAY DIFFRACTION99.98
3.73-28.510.17362500.17144468X-RAY DIFFRACTION99.79

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