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- PDB-9n5h: Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A... -

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Basic information

Entry
Database: PDB / ID: 9n5h
TitleEndogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
Components
  • 2A2 Heavy Chain
  • 2A2 Kappa Chain
  • Gametocyte surface protein P230
  • LMIV230-01 Heavy Chain
  • LMIV230-01 Kappa Chain
  • RUPA-97 Heavy Chain
  • RUPA-97 Kappa Chain
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)
Homo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHeide, F. / 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: Immunity / Year: 2025
Title: Structure of endogenous Pfs230:Pfs48/45 in complex with potent malaria transmission-blocking antibodies.
Authors: Bekkering, E.T. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van ...Authors: Bekkering, E.T. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van Daalen, R.C. / Inklaar, M.R. / Andrade, C.M. / Jansen, P.W.T.C. / Vermeulen, M. / Bousema, T. / Takashima, E. / Rubinstein, J.L. / Kooij, T.W.A. / Jore, M.M. / Julien, J.P.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P230
B: 2A2 Heavy Chain
C: 2A2 Kappa Chain
D: LMIV230-01 Heavy Chain
E: LMIV230-01 Kappa Chain
H: RUPA-97 Heavy Chain
L: RUPA-97 Kappa Chain


Theoretical massNumber of molelcules
Total (without water)505,1057
Polymers505,1057
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

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Protein , 1 types, 1 molecules A

#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

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Antibody , 6 types, 6 molecules BCDEHL

#2: 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)
#3: 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)
#4: Antibody LMIV230-01 Heavy Chain


Mass: 23340.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody LMIV230-01 Kappa Chain


Mass: 23365.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody RUPA-97 Heavy Chain


Mass: 24074.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#7: Antibody RUPA-97 Kappa Chain


Mass: 23511.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Details

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 Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
Type: COMPLEX / Entity ID: #1, #3, #2, #6-#7, #4-#5 / 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 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
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70113 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDSource nameTypeAccession codeInitial refinement model-ID
11AlphaFoldin silico model
27UVQ

7uvq

1PDBexperimental model7UVQ2
37JUM

7jum

1PDBexperimental model7JUM3
49N89

9n89

1PDBexperimental model9N894
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 107.76 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002119553
ELECTRON MICROSCOPYf_angle_d0.565926518
ELECTRON MICROSCOPYf_chiral_restr0.04432972
ELECTRON MICROSCOPYf_plane_restr0.00453389
ELECTRON MICROSCOPYf_dihedral_angle_d4.80972611

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