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- PDB-9e7o: Pfs230 D13D14 in complex with nanobody W2810 -

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Basic information

Entry
Database: PDB / ID: 9e7o
TitlePfs230 D13D14 in complex with nanobody W2810
Components
  • Gametocyte surface protein P230
  • Nanobody W2810
KeywordsPROTEIN BINDING / 6-cysteine protein / Plasmodium falciparum / malaria transmission / nanobody
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 speciesVicugna pacos (alpaca)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDietrich, M.H. / Tan, L.L. / Tham, W.H.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2001385 Australia
National Health and Medical Research Council (NHMRC, Australia)APP2016908 Australia
CitationJournal: Science / Year: 2025
Title: Cryo-EM structure of endogenous Pfs230 and Pfs48/45 fertilization complex.
Authors: Melanie H Dietrich / Jill Chmielewski / Li-Jin Chan / Li Lynn Tan / Amy Adair / Frankie M T Lyons / Mikha Gabriela / Sash Lopaticki / Toby A Dite / Laura F Dagley / Lucia Pazzagli / Priya ...Authors: Melanie H Dietrich / Jill Chmielewski / Li-Jin Chan / Li Lynn Tan / Amy Adair / Frankie M T Lyons / Mikha Gabriela / Sash Lopaticki / Toby A Dite / Laura F Dagley / Lucia Pazzagli / Priya Gupta / Mohd Kamil / Ashley M Vaughan / Rattanaporn Rojrung / Anju Abraham / Ramin Mazhari / Rhea J Longley / Kathleen Zeglinski / Quentin Gouil / Ivo Mueller / Stewart A Fabb / Rekha Shandre-Mugan / Colin W Pouton / Alisa Glukhova / Shabih Shakeel / Wai-Hong Tham /
Abstract: Malaria parasite fertilization occurs in the midgut of a female mosquito. Blocking fertilization within the mosquito can prevent malaria transmission. Pfs230 and Pfs48/45 are critical for male ...Malaria parasite fertilization occurs in the midgut of a female mosquito. Blocking fertilization within the mosquito can prevent malaria transmission. Pfs230 and Pfs48/45 are critical for male fertility and transmission of the malaria parasite. They form a core fertilization complex, but it is unknown how they interact. We determined a cryo-electron microscopy structure of endogenous Pfs230-Pfs48/45 complex showing that Pfs48/45 interacts with Pfs230 domains 13 and 14. Transgenic parasite lines with these domains removed were defective in Pfs230 gamete localization and showed reduced oocyst formation. Nanobodies against domains 13 and 14 inhibited Pfs230-Pfs48/45 complex formation, reduced transmission and structural analyses revealed their epitopes. These Pfs230 domains were targets of naturally acquired immunity and immune sera from mRNA-lipid nanoparticle immunizations blocked parasite transmission.
History
DepositionNov 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _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: Nanobody W2810
B: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1589
Polymers47,0432
Non-polymers1,1157
Water2,306128
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)135.494, 62.824, 56.481
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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Components

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Antibody / Protein , 2 types, 2 molecules AB

#1: Antibody Nanobody W2810


Mass: 13666.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Gametocyte surface protein P230


Mass: 33375.906 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P68874

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Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 132 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.4 M sodium malonate dibasic monohydrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953647 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953647 Å / Relative weight: 1
ReflectionResolution: 1.93→39.92 Å / Num. obs: 35422 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 43.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.088 / Net I/σ(I): 13.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.93-2.050.64256080.7041.3641
2.05-2.190.34253950.8310.8681
2.19-2.360.22749660.9230.5211
2.36-2.590.16146210.9680.3331
2.59-2.890.09641680.9870.1831
2.89-3.330.05336930.9970.0921
3.33-4.080.0331230.9990.0521
4.08-5.750.01924580.9990.0371

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→39.92 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1767 4.99 %
Rwork0.2138 --
obs0.2158 35377 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 72 128 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093288
X-RAY DIFFRACTIONf_angle_d1.0284475
X-RAY DIFFRACTIONf_dihedral_angle_d17.0081208
X-RAY DIFFRACTIONf_chiral_restr0.064504
X-RAY DIFFRACTIONf_plane_restr0.007570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.40361340.35282567X-RAY DIFFRACTION100
1.98-2.040.34061320.29282543X-RAY DIFFRACTION100
2.04-2.110.33081370.27192589X-RAY DIFFRACTION100
2.11-2.180.34161360.2672592X-RAY DIFFRACTION100
2.18-2.270.31351350.25292561X-RAY DIFFRACTION100
2.27-2.370.31831350.23832565X-RAY DIFFRACTION100
2.37-2.50.28091360.24422582X-RAY DIFFRACTION100
2.5-2.650.32511350.24152571X-RAY DIFFRACTION100
2.65-2.860.31841360.23992582X-RAY DIFFRACTION100
2.86-3.150.29581370.23382605X-RAY DIFFRACTION100
3.15-3.60.2381360.21032581X-RAY DIFFRACTION100
3.6-4.530.20391370.18312605X-RAY DIFFRACTION100
4.54-39.920.20391410.17852667X-RAY DIFFRACTION100

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