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- EMDB-48921: Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A... -

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Basic information

Entry
Database: EMDB / ID: EMD-48921
TitleEndogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
Map dataEndogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
Sample
  • Complex: Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
    • Protein or peptide: Gametocyte surface protein P230
    • Protein or peptide: 2A2 Kappa Chain
    • Protein or peptide: 2A2 Heavy Chain
    • Protein or peptide: RUPA-97 Heavy Chain
    • Protein or peptide: RUPA-97 Kappa Chain
    • Protein or peptide: LMIV230-01 Heavy Chain
    • Protein or peptide: LMIV230-01 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) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHeide F / 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_48921.png

Downloads & links

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Map

FileDownload / File: emd_48921.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEndogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 450 pix.
= 418.5 Å		0.93 Å/pix.
x 450 pix.
= 418.5 Å		0.93 Å/pix.
x 450 pix.
= 418.5 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: 0.1
Minimum - Maximum-0.24597634 - 0.5318921
Average (Standard dev.)-0.00021148096 (±0.010414883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 418.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_48921_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48921_half_map_2.map
AnnotationHalf Map A
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 Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A...

EntireName: Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
Components
  • Complex: Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
    • Protein or peptide: Gametocyte surface protein P230
    • Protein or peptide: 2A2 Kappa Chain
    • Protein or peptide: 2A2 Heavy Chain
    • Protein or peptide: RUPA-97 Heavy Chain
    • Protein or peptide: RUPA-97 Kappa Chain
    • Protein or peptide: LMIV230-01 Heavy Chain
    • Protein or peptide: LMIV230-01 Kappa Chain

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Supramolecule #1: Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A...

SupramoleculeName: Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #6-#7, #4-#5
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: 2A2 Heavy Chain

MacromoleculeName: 2A2 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.507283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLQQSGPE LEKPGASVKI SCKASGYSIT DYNMNWVKLS NGKSLEWIGN IDPSHGGTTY NQKFKGKATL TVDKSSSTAY MQLKSLTSE DSAVYHCARS TLYGNSAMDC WGQGTSVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
EVQLQQSGPE LEKPGASVKI SCKASGYSIT DYNMNWVKLS NGKSLEWIGN IDPSHGGTTY NQKFKGKATL TVDKSSSTAY MQLKSLTSE DSAVYHCARS TLYGNSAMDC WGQGTSVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC

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Macromolecule #3: 2A2 Kappa Chain

MacromoleculeName: 2A2 Kappa Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.604301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIVMTQTPKF LLVPAGDRVT ITCKASQSVN NDVTWYQQKP GQSPKLLIYY ASNRYTGVPD RFTGSGYGTD FTFTISTVQA EDLAVYFCQ QDYSSPLTFG AGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
SIVMTQTPKF LLVPAGDRVT ITCKASQSVN NDVTWYQQKP GQSPKLLIYY ASNRYTGVPD RFTGSGYGTD FTFTISTVQA EDLAVYFCQ QDYSSPLTFG AGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: LMIV230-01 Heavy Chain

MacromoleculeName: LMIV230-01 Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.340297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKVSGGTFN TYAIIWVRQA PGQGLEWMGA IIPFQDRGQY AQKFQGRVTI TADKSTSTAY MELSSLRSE DTAVYYCAKE SGRAVADRWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVQSGAE VKKPGSSVKV SCKVSGGTFN TYAIIWVRQA PGQGLEWMGA IIPFQDRGQY AQKFQGRVTI TADKSTSTAY MELSSLRSE DTAVYYCAKE SGRAVADRWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSC

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Macromolecule #5: LMIV230-01 Kappa Chain

MacromoleculeName: LMIV230-01 Kappa Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.3651 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPAS LALSLGERAT LYCRASHSIS SWLAWYQQKP GKAPKLLIYK ASTLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYKSYPWTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIVMTQSPAS LALSLGERAT LYCRASHSIS SWLAWYQQKP GKAPKLLIYK ASTLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYKSYPWTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRG

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Macromolecule #6: RUPA-97 Heavy Chain

MacromoleculeName: RUPA-97 Heavy Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.074934 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVENGGG LVKPGGSLRL SCAASGFTIS SYGMNWVRQA PGKGLEWVSS ISSGSTYKYY SDSVKGRFTI SRDNAKNSLY LQMNTLRAE DTAVYYCARA PEPGLTWFGE WGDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLVENGGG LVKPGGSLRL SCAASGFTIS SYGMNWVRQA PGKGLEWVSS ISSGSTYKYY SDSVKGRFTI SRDNAKNSLY LQMNTLRAE DTAVYYCARA PEPGLTWFGE WGDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSC

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Macromolecule #7: RUPA-97 Kappa Chain

MacromoleculeName: RUPA-97 Kappa Chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.511209 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPVT LSLSPGERAT LSCRASLSIS SSLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSIWPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPVT LSLSPGERAT LSCRASLSIS SSLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSIWPPITF GQGTRLEIKR 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 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMKClpotassium chloride
GridModel: Homemade / Material: GOLD
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
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.0) / Number images used: 70113
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
source_name: AlphaFold, initial_model_type: in silico model
source_name: PDB, initial_model_type: experimental model

7uvq

source_name: PDB, initial_model_type: experimental model

7jum

source_name: PDB, initial_model_type: experimental model

9n89

SoftwareName: UCSF ChimeraX (ver. 1.9)
Output model

PDB-9n5h:
Endogenous Pfs230D1-6 in complex with RUPA-97, LMIV230-01, and 2A2 Fab domains

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