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- EMDB-48922: Endogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pf... -

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Basic information

Entry
Database: EMDB / ID: EMD-48922
TitleEndogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Map dataEndogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Sample
  • Complex: Endogenous Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
    • Protein or peptide: Gametocyte surface protein P230
    • Protein or peptide: Gametocyte surface protein P45/48
    • Protein or peptide: RUPA-44 Fab kappa chain
    • Protein or peptide: RUPA-44 Fab heavy chain
    • Protein or peptide: RUPA-71 Fab heavy chain
    • Protein or peptide: RUPA-71 Fab kappa chain
KeywordsPfs48/45 / Pfs230 / Malaria / transmission-blocking antibodies / IMMUNE SYSTEM
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane
Similarity search - Function
: / 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
Similarity search - Domain/homology
Gametocyte surface protein P230 / Gametocyte surface protein P45/48
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsHailemariam S / Heide F / Bekkering E / Ivanochko D / Yoo R / Julien JP
Funding support Canada, 1 items
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: Bekkering E / Yoo R / Hailemariam S / Heide F / Ivanochko D / Jackman M / Proellochs N / Stoter R / van Gemert GJ / Maeda A / Yuguchi T / Wanders O / van Daalen R / Inklaar M / Andrade C / ...Authors: Bekkering E / Yoo R / Hailemariam S / Heide F / Ivanochko D / Jackman M / Proellochs N / Stoter R / van Gemert GJ / Maeda A / Yuguchi T / Wanders O / van Daalen R / Inklaar M / Andrade C / Jansen P / Vermeulen M / Bousema T / Takashima E / Rubinstein J / Kooij T / Jore M / 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_48922.png

Downloads & links

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Map

FileDownload / File: emd_48922.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEndogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 500 pix.
= 465. Å		0.93 Å/pix.
x 500 pix.
= 465. Å		0.93 Å/pix.
x 500 pix.
= 465. 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: 0.18
Minimum - Maximum-1.0226549 - 1.5359708
Average (Standard dev.)-0.00010475635 (±0.018591918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 465.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48922_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_48922_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48922_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_48922_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 Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45...

EntireName: Endogenous Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
Components
  • Complex: Endogenous Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
    • Protein or peptide: Gametocyte surface protein P230
    • Protein or peptide: Gametocyte surface protein P45/48
    • Protein or peptide: RUPA-44 Fab kappa chain
    • Protein or peptide: RUPA-44 Fab heavy chain
    • Protein or peptide: RUPA-71 Fab heavy chain
    • Protein or peptide: RUPA-71 Fab kappa chain

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Supramolecule #1: Endogenous Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45...

SupramoleculeName: Endogenous Pfs230 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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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 (malaria parasite P. falciparum)
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: Gametocyte surface protein P45/48

MacromoleculeName: Gametocyte surface protein P45/48 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 51.545887 KDa
SequenceString: MMLYISAKKA QVAFILYIVL VLRIISGNND FCKPSSLNSE ISGFIGYKCN FSNEGVHNLK PDMRERRSIF CTIHSYFIYD KIRLIIPKK SSSPEFKILP EKCFQKVYTD YENRVETDIS ELGLIEYEIE ENDTNPNYNE RTITISPFSP KDIEFFCFCD N TEKVISSI ...String:
MMLYISAKKA QVAFILYIVL VLRIISGNND FCKPSSLNSE ISGFIGYKCN FSNEGVHNLK PDMRERRSIF CTIHSYFIYD KIRLIIPKK SSSPEFKILP EKCFQKVYTD YENRVETDIS ELGLIEYEIE ENDTNPNYNE RTITISPFSP KDIEFFCFCD N TEKVISSI EGRSAMVHVR VLKYPHNILF TNLTNDLFTY LPKTYNESNF VSNVLEVELN DGELFVLACE LINKKCFQEG KE KALYKSN KIIYHKNLTI FKAPFYVTSK DVNTECTCKF KNNNYKIVLK PKYEKKVIHG CNFSSNVSSK HTFTDSLDIS LVD DSAHIS CNVHLSEPKY NHLVGLNCPG DIIPDCFFQV YQPESEELEP SNIVYLDSQI NIGDIEYYED AEGDDKIKLF GIVG SIPKT TSFTCICKKD KKSAYMTVTI DSAYYGFLAK TFIFLIVAIL LYI

UniProtKB: Gametocyte surface protein P45/48

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Macromolecule #3: RUPA-44 Fab kappa chain

MacromoleculeName: RUPA-44 Fab kappa chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.483105 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPAT LSASVGDRVT ITCRASQSIS SWLAWYQQKP GEAPKLLIYK ASSLQSGVPS RFSGSGSGTK FSLTISSLQP DDFATFYCQ QYHSYPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPAT LSASVGDRVT ITCRASQSIS SWLAWYQQKP GEAPKLLIYK ASSLQSGVPS RFSGSGSGTK FSLTISSLQP DDFATFYCQ QYHSYPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: RUPA-44 Fab heavy chain

MacromoleculeName: RUPA-44 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.277332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLQLQESGPG LVKPSETLSL TCTVSGGSIS RSPYYWGWIR QPPGKGLEWF GSIYNNGSTY YNPPLKSRLT ISVDTSKNQF SLKLSSVTA ADTAVYYCAR HGGSTGMKVV VIAPPDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QLQLQESGPG LVKPSETLSL TCTVSGGSIS RSPYYWGWIR QPPGKGLEWF GSIYNNGSTY YNPPLKSRLT ISVDTSKNQF SLKLSSVTA ADTAVYYCAR HGGSTGMKVV VIAPPDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC

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Macromolecule #5: RUPA-71 Fab heavy chain

MacromoleculeName: RUPA-71 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.711725 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEQLVESGGG LVKPGRSLRL SCSASGFTLG DYAVTWFRQA SGKEPEWVGV IRTKDEGGTT EYAASVKGRF SILRDDSKSI AHLQMNSLK IEDTAVYYCT RNGLRWYDSS GPRGWAFDIW GPGTLVVVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
EEQLVESGGG LVKPGRSLRL SCSASGFTLG DYAVTWFRQA SGKEPEWVGV IRTKDEGGTT EYAASVKGRF SILRDDSKSI AHLQMNSLK IEDTAVYYCT RNGLRWYDSS GPRGWAFDIW GPGTLVVVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSC

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Macromolecule #6: RUPA-71 Fab kappa chain

MacromoleculeName: RUPA-71 Fab kappa chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.598248 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPAT VSVSPGERAT LSCRTSQSVS NKLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTQ FTLTISSLQS EDFAVYYCQ QYNNWPPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPAT VSVSPGERAT LSCRTSQSVS NKLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTQ FTLTISSLQS EDFAVYYCQ QYNNWPPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic 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
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average exposure time: 6.5 sec. / Average electron dose: 52.0 e/Å2
Details: Images were collected at average electron doses per image of 50 and 53.7 electrons per square Angstrom 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 model#0 - Type of model: NONE / #1 - Type of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.0) / Number images used: 146814
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8u1p

source_name: PDB, initial_model_type: experimental model

7uxl

source_name: PDB, initial_model_type: experimental model

9n7k

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-9n5i:
Endogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44

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