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- EMDB-48941: Endogenous Pfs230D7-8 in complex with 18F25 -

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Basic information

Entry
Database: EMDB / ID: EMD-48941
TitleEndogenous Pfs230D7-8 in complex with 18F25
Map dataEndogenous Pfs230D7-8 in complex with 18F25
Sample
  • Complex: Endogenous Pfs230D7-8 in complex with 18F25
    • Protein or peptide: Gametocyte surface protein P230
    • Protein or peptide: 18F25 Heavy Chain
    • Protein or peptide: 18F25 Kappa Chain
Keywords6-Cys / antibody / IMMUNE SYSTEM
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 speciesPlasmodium falciparum 3D7 (eukaryote) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsJackman JJ / Yoo R / Ivanochko D / Hailemariam S / Bekkering E / Julien JP
Funding support Canada, 1 items
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 ET / Yoo R / Hailemariam S / Heide F / Ivanochko D / Jackman M / Proellochs NI / Stoter R / van Gemert GJ / Maeda A / Yuguchi T / Wanders OT / van Daalen RC / Inklaar MR / Andrade ...Authors: Bekkering ET / Yoo R / Hailemariam S / Heide F / Ivanochko D / Jackman M / Proellochs NI / Stoter R / van Gemert GJ / Maeda A / Yuguchi T / Wanders OT / van Daalen RC / Inklaar MR / Andrade CM / Jansen PWTC / Vermeulen M / Bousema T / Takashima E / Rubinstein JL / Kooij TWA / Jore MM / Julien JP
History
DepositionFeb 4, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48941.png

Downloads & links

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Map

FileDownload / File: emd_48941.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEndogenous Pfs230D7-8 in complex with 18F25
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0597
Minimum - Maximum-0.24064481 - 0.8917581
Average (Standard dev.)0.00076595636 (±0.008657658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_48941_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48941_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Endogenous Pfs230D7-8 in complex with 18F25

EntireName: Endogenous Pfs230D7-8 in complex with 18F25
Components
  • Complex: Endogenous Pfs230D7-8 in complex with 18F25
    • Protein or peptide: Gametocyte surface protein P230
    • Protein or peptide: 18F25 Heavy Chain
    • Protein or peptide: 18F25 Kappa Chain

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Supramolecule #1: Endogenous Pfs230D7-8 in complex with 18F25

SupramoleculeName: Endogenous Pfs230D7-8 in complex with 18F25 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Macromolecule #1: Gametocyte surface protein P230

MacromoleculeName: Gametocyte surface protein P230 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 363.70175 KDa
SequenceString: MKKIITLKNL FLIILVYIFS EKKDLRCNVI KGNNIKDDED KRFHLFYYSH NLFKTPETKE KKNKKECFYK NGGIYNLSKE IRMRKDTSV KIKQRTCPFH KEGSSFEMGS KNITCFYPIV GKKERKTLDT IIIKKNVTND HVVSSDMHSN VQEKNMILIR N IDKENKND ...String:
MKKIITLKNL FLIILVYIFS EKKDLRCNVI KGNNIKDDED KRFHLFYYSH NLFKTPETKE KKNKKECFYK NGGIYNLSKE IRMRKDTSV KIKQRTCPFH KEGSSFEMGS KNITCFYPIV GKKERKTLDT IIIKKNVTND HVVSSDMHSN VQEKNMILIR N IDKENKND IQNVEEKIQR DTYENKDYES DDTLIEWFDD NTNEENFLLT FLKRCLMKIF SSPKRKKTVV QKKHKSNFFI NS SLKYIYM YLTPSDSFNL VRRNRNLDEE DMSPRDNFVI DDEEEEEEEE EEEEEEEEEE EEEEEEEYDD YVYEESGDET EEQ LQEEHQ EEVGAESSEE SFNDEDEDSV EARDGDMIRV DEYYEDQDGD TYDSTIKNED VDEEVGEEVG EEVGEEVGEE VGEE VGEEV GEEVGEEVGE EEGEEVGEGV GEEVGEEEGE EVGEEEGEYV DEKERQGEIY PFGDEEEKDE GGESFTYEKS EVDKT DLFK FIEGGEGDDV YKVDGSKVLL DDDTISRVSK KHTARDGEYG EYGEAVEDGE NVIKIIRSVL QSGALPSVGV DELDKI DLS YETTESGDTA VSEDSYDKYA SNNTNKEYVC DFTDQLKPTE SGPKVKKCEV KVNEPLIKVK IICPLKGSVE KLYDNIE YV PKKSPYVVLT KEETKLKEKL LSKLIYGLLI SPTVNEKENN FKEGVIEFTL PPVVHKATVF YFICDNSKTE DDNKKGNR G IVEVYVEPYG NKINGCAFLD EDEEEEKYGN QIEEDEHNEK IKMKTFFTQN IYKKNNIYPC YMKLYSGDIG GILFPKNIK STTCFEEMIP YNKEIKWNKE NKSLGNLVNN SVVYNKEMNA KYFNVQYVHI PTSYKDTLNL FCSIILKEEE SNLISTSYLV YVSINEELN FSLFDFYESF VPIKKTIQVA QKNVNNKEHD YTCDFTDKLD KTVPSTANGK KLFICRKHLK EFDTFTLKCN V NKTQYPNI EIFPKTLKDK KEVLKLDLDI QYQMFSKFFK FNTQNAKYLN LYPYYLIFPF NHIGKKELKN NPTYKNHKDV KY FEQSSVL SPLSSADSLG KLLNFLDTQE TVCLTEKIRY LNLSINELGS DNNTFSVTFQ VPPYIDIKEP FYFMFGCNNN KGE GNIGIV ELLISKQEEK IKGCNFHESK LDYFNENISS DTHECTLHAY ENDIIGFNCL ETTHPNEVEV EVEDAEIYLQ PENC FNNVY KGLNSVDITT ILKNAQTYNI NNKKTPTFLK IPPYNLLEDV EISCQCTIKQ VVKKIKVIIT KNDTVLLKRE VQSES TLDD KIYKCEHENF INPRVNKTFD ENVEYTCNIK IENFFNYIQI FCPAKDLGIY KNIQMYYDIV KPTRVPQFKK FNNEEL HKL IPNSEMLHKT KEMLILYNEE KVDLLHFYVF LPIYIKDIYE FNIVCDNSKT MWKNQLGGKV IYHITVSKRE QKVKGCS FD NEHAHMFSYN KTNVKNCIID AKPKDLIGFV CPSGTLKLTN CFKDAIVHTN LTNINGILYL KNNLANFTYK HQFNYMEI P ALMDNDISFK CICVDLKKKK YNVKSPLGPK VLRALYKKLN IKFDNYVTGT DQNKYLMTYM DLHLSHKRNY LKELFHDLG KKKPADTDAN PESIIESLSI NESNESGPFP TGDVDAEHLI LEGYDTWESL YDEQLEEVIY NDIESLELKD IEQYVLQVNL KAPKLMMSA QIHNNRHVCD FSKNNLIVPE SLKKKEELGG NPVNIHCYAL LKPLDTLYVK CPTSKDNYEA AKVNISENDN E YELQVISL IEKRFHNFET LESKKPGNGD VVVHNGVVDT GPVLDNSTFE KYFKNIKIKP DKFFEKVINE YDDTEEEKDL ES ILPGAIV SPMKVLKKKD PFTSYAAFVV PPIVPKDLHF KVECNNTEYK DENQYISGYN GIIHIDISNS NRKINGCDFS TNN SSILTS SVKLVNGETK NCEININNNE VFGIICDNET NLDPEKCFHE IYSKDNKTVK KFREVIPNID IFSLHNSNKK KVAY AKVPL DYINKLLFSC SCKTSHTNTI GTMKVTLNKD EKEEEDFKTA QGIKHNNVHL CNFFDNPELT FDNNKIVLCK IDAEL FSEV IIQLPIFGTK NVEEGVQNEE YKKFSLKPSL VFDDNNNDIK VIGKEKNEVS ISLALKGVYG NRIFTFDKNG KKGEGI SFF IPPIKQDTDL KFIINETIDN SNIKQRGLIY IFVRKNVSEN SFKLCDFTTG STSLMELNSQ VKEKKCTVKI KKGDIFG LK CPKGFAIFPQ ACFSNVLLEY YKSDYEDSEH INYYIHKDKK YNLKPKDVIE LMDENFRELQ NIQQYTGISN ITDVLHFK N FNLGNLPLNF KNHYSTAYAK VPDTFNSIIN FSCNCYNPEK HVYGTMQVES DNRNFDNIKK NENVIKNFLL PNIEKYALL LDDEERQKKI KQQQEEEQQE QILKDQDDRL SRHDDYNKNH TYILYDSNEH ICDYEKNESL ISTLPNDTKK IQKSICKINA KALDVVTIK CPHTKNFTPK DYFPNSSLIT NDKKIVITFD KKNFVTYIDP TKKTFSLKDI YIQSFYGVSL DHLNQIKKIH E EWDDVHLF YPPHNVLHNV VLNNHIVNLS SALEGVLFMK SKVTGDETAT KKNTTLPTDG VSSILIPPYV KEDITFHLFC GK STTKKPN KKNTSLALIH IHISSNRNII HGCDFLYLEN QTNDAISNNN NNSYSIFTHN KNTENNLICD ISLIPKTVIG IKC PNKKLN PQTCFDEVYY VKQEDVPSKT ITADKYNTFS KDKIGNILKN AISINNPDEK DNTYTYLILP EKFEEELIDT KKVL ACTCD NKYIIHMKIE KSTMDKIKID EKKTIGKDIC KYDVTTKVAT CEIIDTIDSS VLKEHHTVHY SITLSRWDKL IIKYP TNEK THFENFFVNP FNLKDKVLYN YNKPINIEHI LPGAITTDIY DTRTKIKQYI LRIPPYVHKD IHFSLEFNNS LSLTKQ NQN IIYGNVAKIF IHINQGYKEI HGCDFTGKYS HLFTYSKKPL PNDDDICNVT IGNNTFSGFA CLSHFELKPN NCFSSVY DY NEANKVKKLF DLSTKVELDH IKQNTSGYTL SYIIFNKEST KLKFSCTCSS NYSNYTIRIT FDPNYIIPEP QSRAIIKY V DLQDKNFAKY LRKL

UniProtKB: Gametocyte surface protein P230

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Macromolecule #2: 18F25 Heavy Chain

MacromoleculeName: 18F25 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.50332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGAE LARPGASVKL SCKASGYTFT NYWMQWVKQR PGQGLEWFGA IYPGDGDTRY TQKFKGKATL TADKSSSTAY MQLSSLASE DSAVYYCARS LYLGAMDYWG QGTSVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLQQSGAE LARPGASVKL SCKASGYTFT NYWMQWVKQR PGQGLEWFGA IYPGDGDTRY TQKFKGKATL TADKSSSTAY MQLSSLASE DSAVYYCARS LYLGAMDYWG QGTSVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSC

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Macromolecule #3: 18F25 Kappa Chain

MacromoleculeName: 18F25 Kappa Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.530119 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSHKF MSTSVGDRVS ITCKASQDVT NDVAWYQQKP GQSPKLLIYS ASYRYTGVPD RFTGSGSGTD FIFTISSVQA EDLAVYYCQ QHYSAPPTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVT NDVAWYQQKP GQSPKLLIYS ASYRYTGVPD RFTGSGSGTD FIFTISSVQA EDLAVYYCQ QHYSAPPTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMKClpotassium chloride
GridModel: Homemade / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
Details: The Leica Automatic Plunge Freezer EM GP2 was used for freezing..

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: OTHER / Average exposure time: 6.5 sec. / Average electron dose: 52.0 e/Å2
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.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.0) / Number images used: 137749
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: AlphaFold, initial_model_type: in silico modelmodel generated in-house
source_name: PDB, initial_model_type: experimental model

9n6u

SoftwareName: UCSF ChimeraX (ver. 1.9)
Output model

PDB-9n5o:
Endogenous Pfs230D7-8 in complex with 18F25

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