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- EMDB-72927: Plasmodium falciparum moving junction staple - PfAMA1, PfRON2, Pf... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72927
TitlePlasmodium falciparum moving junction staple - PfAMA1, PfRON2, PfRON4, PfRON5
Map dataComposite map of PfAMA1-RON2/4/5
Sample
  • Complex: Plasmodium falciparum moving junction staple with PfAMA1 - PfRON2 - PfRON4 - PfRON5
    • Protein or peptide: Rhoptry neck protein 2
    • Protein or peptide: Rhoptry neck protein 4
    • Protein or peptide: Rhoptry neck protein 5
    • Protein or peptide: Apical membrane antigen 1
KeywordsInvasion / Plasmodium / Apicomplexa / CryoEM / Endogenous / MEMBRANE PROTEIN
Function / homology
Function and homology information


Domain of unknown function DUF676, lipase-like / Putative serine esterase (DUF676) / Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Domain/homology
Rhoptry neck protein 5 / Rhoptry neck protein 4 / Rhoptry neck protein 2 / Apical membrane antigen 1
Similarity search - Component
Biological speciesPlasmodium falciparum NF54 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHaile MT / Zhen J / Ho C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD029613 United States
CitationJournal: Cell / Year: 2026
Title: Structural basis for host membrane binding and remodeling by invading malaria parasites.
Authors: Meseret T Haile / Daphne A Kaxiras / James Zhen / Carolyn L Lee / Britney Jiang / Jennifer L Small-Saunders / Chi-Min Ho /
Abstract: The Plasmodium moving junction is central to malarial host-cell invasion, and yet its function remains unclear. Here, we determine the endogenous structure of the basic repeating unit of the moving ...The Plasmodium moving junction is central to malarial host-cell invasion, and yet its function remains unclear. Here, we determine the endogenous structure of the basic repeating unit of the moving junction, purified directly from invasion-stalled Plasmodium falciparum parasites, revealing a sailboat-shaped 1:1:1:1 assembly of apical membrane antigen 1 (PfAMA1) and rhoptry neck proteins 2, 4, and 5 (PfRON2, PfRON4, and PfRON5). We observe two PfRON2 transmembrane helices that anchor the complex in the red blood cell (RBC) membrane and display an extracellular handle for PfAMA1 binding. PfAMA1 directly contacts the RBC membrane, strengthening the connection. PfRON2/4/5 form a large, basic platform inside the RBC that electrostatically engages the RBC membrane and wedges seven amphipathic helices deep into the bilayer, suggesting an active role in host-membrane remodeling. We then leverage the native membrane context revealed by our structure, along with recent advances in computational protein design, to enable the rational design of a small protein binder that inhibits invasion.
History
DepositionSep 29, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72927.png

Downloads & links

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Map

FileDownload / File: emd_72927.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of PfAMA1-RON2/4/5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 600 pix.
= 493.8 Å		0.82 Å/pix.
x 600 pix.
= 493.8 Å		0.82 Å/pix.
x 600 pix.
= 493.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.887
Minimum - Maximum-0.0842819 - 6.9616995
Average (Standard dev.)0.018961744 (±0.07683178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 493.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Plasmodium falciparum moving junction staple with PfAMA1 - PfRON2...

EntireName: Plasmodium falciparum moving junction staple with PfAMA1 - PfRON2 - PfRON4 - PfRON5
Components
  • Complex: Plasmodium falciparum moving junction staple with PfAMA1 - PfRON2 - PfRON4 - PfRON5
    • Protein or peptide: Rhoptry neck protein 2
    • Protein or peptide: Rhoptry neck protein 4
    • Protein or peptide: Rhoptry neck protein 5
    • Protein or peptide: Apical membrane antigen 1

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Supramolecule #1: Plasmodium falciparum moving junction staple with PfAMA1 - PfRON2...

SupramoleculeName: Plasmodium falciparum moving junction staple with PfAMA1 - PfRON2 - PfRON4 - PfRON5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)

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Macromolecule #1: Rhoptry neck protein 2

MacromoleculeName: Rhoptry neck protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 249.80175 KDa
SequenceString: MLKFFIFILH IYLYIDSIYS SELSKHVKHD TDELKYASPT YDPKKGTKVI FYMPGNEQGV IPNNIQNKQH GTSIYPAIEY PTTKYPAIE YPGSEMNNGK TGTTNSGIYN KAHGSSNDYN ASNSQDKTIN LHIDENNSNN SYQPYDSNNT NNNTNSNNNS N NNSNNNSN ...String:
MLKFFIFILH IYLYIDSIYS SELSKHVKHD TDELKYASPT YDPKKGTKVI FYMPGNEQGV IPNNIQNKQH GTSIYPAIEY PTTKYPAIE YPGSEMNNGK TGTTNSGIYN KAHGSSNDYN ASNSQDKTIN LHIDENNSNN SYQPYDSNNT NNNTNSNNNS N NNSNNNSN NNSNNYSNNN SNTNSNTNSN TNSNNNTTNY DLNSEYEKIR RKEEEAARRI ERERRADINR KNQDNNSNKY NN EQNGGYE SDGNSPNSRV NINITNNGTH GNPHNNNSYG HKNNMHNTTN GNYANGNYAN GNYSKGDYTN GDYTNGDYTN GDY TNGINN NMHGKNNYNT ANGEYVNGAY DGLNNGSYKL IGNLNNNQNV DNSYNQGNEN DKTYTSNYNI NLEDNKNSPD NNQN YISTF NKDIGPNKSE RSYYDVYGRE YDDNKYNPYN KTNNHNTNQN GSTTYGSNAN GTYGPNGTYG SNGTYEPNES YGPNG AYGP NGTYGHNGKY GSKGTYGNNE TPYYVEHPEY DNGKSMSDFH VKDSKDNIGP GGDYPNLYQN IYGNEKNPNI FPGSPR NIN VYSVHHIPNN GANGGLNSGA NGGLNNGAND GLNNGANGGL NNGANGGLNN GANGGLNNGM NNGMNNGMNN GMNNGMN NG MNNGMNNGTN GGLNNGMNNG MNNGMNNGMN NGIHDDLYNS ENSTFNNGLN NSGRTGLNNA YPHNGMLNNG TEYNVHYG N SDSNNTNDSM LNENYYSDSD YDDHTPGNKK KVYKSVAERN KKSASQDSLG AGFSDSDSDS EYEVVDGENK KYKKKNKEN NEKDKYENNW DSNNYNSDNE IKDGYLSESE REYARNKANE IEDKMKKGEY SRKYKNSKSN ESGYASKQTS DSDDSDIEAN AFYVDNGQE MLIKEKEHYS SDSEHHKEES ASIGNLNVFF PAENYHFSTY MGFDRRSFLP SNEIELEKMI GANFSNEVKN Y CSRQNVAQ KIGDYLNISF EYSRALEELR SEMILDFNKR KHLTNNTDDT ILHMIENAEK RKNDPNYKEA YENKDYANNA NI FMNEYSN PLSTKYNKIL KEYLCHLFVN NPGTKPLERL YYNSLALGEL VEPIRNKFKS LASSTIDFNY EIHMASASNI YLL AHFLVL SLAYLSYNEY FTTGTKSFYS LPTILTANSD NSFFMLNEMC NIHYNPNKNF KKDITFIPIE SRPKRTTTFY GERR LTCDL LELVLNAIML ININEINNVF SNNNVDGYEN SLSFSHNAIR IFSKVCPKIN NDNVLKCEFE ESSLYNPKII KNDTS EKSS QKNLKKAFDL LRTYAEIEGH SAEGSTSPYY VSLILDDMKY NDFYKYTLWY EPRELIYGDI RGMQMKKKKK TKYIYN DFM KKSTQLKKKL IKNDLKYNLK SKGLVFLYAM IDKYGSILNK SQKAKVQFLN STSSIRYYLY LNKVIFKSAK TYLDIMK RV LEELQTSTNT PLKFLVRGNY IENINNIARN DNMFYANLFV LTALSRRDPV KDYYNDKRKM LSATLAEKFA NSTSMLIP H KLRKLVVSMK KGLLKKKLLT SLAKVKLLQH IPAHMLENIT SSIRFTTHTI ATMQIIQNAK YMSKHNFSQY DSKGMLARQ IFTKGGFAEY ADNLMAKWFS KGFEEYKREQ IENFKMENSI DSELKDSERE DENDSSEESA KKKLQDLQLE EREKMKKENS LLFNQSDKW DQFINKELVR ALGLWLEFND NPTNASSFVY KVVEDSKHLL ENNIDNNIIF SRTVKPTKQT AFRRFFNKIL S LGNMLLRK PSFRVEHALW FGATIDIKKA FILLEKVSEL HKMLNNQDES WLINEAFIEI VDHVVDLSTY KHVREPFGVA RN PGMMAIN PKYAELSHEN RLRELQNSMC ADHCSSVWKV ISSFALHHLK NPDSLHTYES KFSKNSFGNK IDDKDFVHNF KMI LGGDAV LHYFDNLLPK TMKKDLKAMK YGVSLTSAYS LKLTKIIFSQ MQLPYLSQMF YMQAPYFGHF IGKWQKKRQQ SRLK EIMSF MTLGSLSAYT LFSAMDITQQ AKDIGAGPVA SCFTTRMSPP QQICLNSVVN TALSTSTQSA MKCVFSVGLF ASIGP YLFA PMAGLAVWNI LKSEFKVLQR IDMALKNVFK NMWNKFLSLK GISKLRGIFK RKKAMKKKII ENATRKMNDM KNNPEK AKA HKMALKKINN YSKGSYHYIS YAKIRI

UniProtKB: Rhoptry neck protein 2

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Macromolecule #2: Rhoptry neck protein 4

MacromoleculeName: Rhoptry neck protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 135.755219 KDa
SequenceString: MSSVRFFLCI FLVLFTFIDI VKPFKGNYGE ANFSFFQATP ASHIEEPQKT ESTDAQSNIT QNEEINNTKP LQENITNNQQ NSNEQQNNN EQQNNIEQQN NNIQQNNIDT SISHVPNDTI KNPIDNSNIS NLDKSNDTNN VIKHEENNQT KENNLETIKH T EPLTNQNT ...String:
MSSVRFFLCI FLVLFTFIDI VKPFKGNYGE ANFSFFQATP ASHIEEPQKT ESTDAQSNIT QNEEINNTKP LQENITNNQQ NSNEQQNNN EQQNNIEQQN NNIQQNNIDT SISHVPNDTI KNPIDNSNIS NLDKSNDTNN VIKHEENNQT KENNLETIKH T EPLTNQNT NEVKINDHNE HEKNTEENKI EEQYNNINHH SHDINKNQSI NNNMNNENAD KNVPHLDQSA MSNEKHINEH TT NHPIESH TGENNHDKIN EPIPIEHATT PTNEPIPIEH AATPTNEPIP IEHAATPTNE PIHIEHVATP ANEPTHSEHA TTT TNEPIH IEHAATPTNE HIHNEHATTT TNEPTHNEHA ATITHEPTHN EHTTTPTNEP IHNEHATTPT NEPIPIEHIA TPAN EPTHN EHATTTTNEP THNEHTTTPT NEPIHNEHAT TPTNEPIPIE HIATPANEPT HNEHATTTTN EPTHNEHATT TTNEP THNE HATTTTNEPI HNEHATATTN ESTHNEHATT TTNEPTHNEH STTPTNESTH SENATTSTNE QHSHDQNTEV HPNDKL ALV PFQGIKNPIP SNESQPIISF PNEDDNHAQN EGSINAPSEG EHNNTDNKEG PIITPLEGEQ AGTAHKEDVT HKHMVGE HV PPQKTHHGPI ITPVGGNHVP PQTHHAHIIT PVGGEHAHGQ GNNDTTYVTM NTDESSSSDT KGEHSNLRSY NKNMNNNH A QRDQYDSDTL NSEGSDDAYS SMQQNFEKNG IDSFKGKGLH VSLRERIIIE IMESAKNGID GLLKLKDSKD SGKLFMEAL EKLNINMKDL KKDKNLISLE VYDKILSTMF KILTEMSFYE DSKFYETLGI KKDILNQSLK DIKIKMLRKL GVSYSRLPPI IKHTEGKCA IKDIIISISS KELAQRMAIM FTKWLAPDEY GAVVDYENNV ELNVLCSGAP ILIQQWKYYQ NMLGFEEDKD H AYLGLIDE LLVMNKRYSQ NKDYVETLEK IKKSKVFKHC TKIMRIGGKV SSVPFNYENV KKPSSSIIGS LGNLIKANIS TY YKATAQR INSYFHYTEK KSKKSSPLKI ISVCTLLHLT DMLYKCSDEN SNGVMDLYNL QLNTLNMKGK MVLQYLVHLK FLT QEKKNQ LKEICEPQNG LIDETLTKML ILLSTDSHEL LSHELENKGF DEDYIQDEIK NINESDNNIR DKEEDDAEKM IFDD L

UniProtKB: Rhoptry neck protein 4

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Macromolecule #3: Rhoptry neck protein 5

MacromoleculeName: Rhoptry neck protein 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 133.892 KDa
SequenceString: MLKYTLLIYI IAGYFISEIS NKLFDTLLPR NVFKKPKPFK KNEIKKGIDK DEKSIMKNVD SIDVMFEPRV KRFVPSRTRK THVVGGLSQ SIPDPGDVEK SKYEKAVRFF ENIKNEMINM SSKINKQLDS QDISSLNNFK RASEVLKESL ATMHSLDIIR N DGSVDFSK ...String:
MLKYTLLIYI IAGYFISEIS NKLFDTLLPR NVFKKPKPFK KNEIKKGIDK DEKSIMKNVD SIDVMFEPRV KRFVPSRTRK THVVGGLSQ SIPDPGDVEK SKYEKAVRFF ENIKNEMINM SSKINKQLDS QDISSLNNFK RASEVLKESL ATMHSLDIIR N DGSVDFSK YTLDWYSKAN MREKYSIEKS IQKIMNKLFK KARKKKKNMK KKKIDANIEQ LEMDLLVQKF ITENLNASKL LK LYDDSAN DYVSPMHTDV CGQLGSIIFS YMFEKAYKSS INHDISYFQK YLPRLKYRIQ NMIQKGTLLL LEKGLDDSLY TFK SKISDI MEKKFGFNDM CTDKCMDETI KADYDLSEYK NEFSPSKTAQ RRADLVKLLM YYYRDKIYNI ETSADVVLIM LLYL NSANE LSEKGYLDVS SISTDDEFNL INKTIDRSHK FNKKIKIKKK TFFKIAPFNF FREETQEKTG NESIFAIDDI IKTSL LAKK SQNYNSLYET TKDLWNQIQN MYSASYGFVQ SKKIKTNKFV GSKIRNVGFL LRWFNYNKTP SKNINFLVNN FSPLVS ISL QLVFFITTMI EQYESSFLGN FSSALKKIFT LGKSGRNPRN YNDLVNFSEV DYLLRTSKAN NVQRIIMQII RMLKKKF LS SSYTPTLLAQ YMSIFLSLWV FEGENNISLQ NPNISRFKKI FFLTYFVHEK GPVEKAVDII YNKCRMKTDK IVLGCIHD Y GGREKKKLLG LISRKCKPTK ISIRKRSIRK ILNKLMSSLN DPVDILRIAV DTATRCDHFN RSKNIDNVKT KKNKINYEI FVKSELSIRY ICADVTKNVV KKIIRDVSRL KNMREAQNVI DNGLNSVQYL KIRNYRDKES SFTILCPFME GNDKNIRELE RTQISLFIH KNIGMSRIIK GKLINIFKKT LNMREGIKSD SAISIKVGAR KYNGIIFTGG YQLNVDNLDQ NTLHIGLSKT R KVYDGRKY VDELEILKGD GVKNIYMKGL NEDNERIYEL QNNMRVSEFD YAIQNPEANI IVFDGNNYIS SYALRNMGLE HE RIVWAGP SVGWTAEFAL SAISDNPLPI FDGSAWVLLE KLSIRSILGK HLPSDVNGNS LANTVNFVIL NKDGKPILKN TTP VINLKY ATFTLSGIVN FVIKAEKGIG NEIIVHTRIP

UniProtKB: Rhoptry neck protein 5

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Macromolecule #4: Apical membrane antigen 1

MacromoleculeName: Apical membrane antigen 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 72.135734 KDa
SequenceString: MRKLYCVLLL SAFEFTYMIN FGRGQNYWEH PYQNSDVYRP INEHREHPKE YEYPLHQEHT YQQEDSGEDE NTLQHAYPID HEGAEPAPQ EQNLFSSIEI VERSNYMGNP WTEYMAKYDI EEVHGSGIRV DLGEDAEVAG TQYRLPSGKC PVFGKGIIIE N SNTTFLTP ...String:
MRKLYCVLLL SAFEFTYMIN FGRGQNYWEH PYQNSDVYRP INEHREHPKE YEYPLHQEHT YQQEDSGEDE NTLQHAYPID HEGAEPAPQ EQNLFSSIEI VERSNYMGNP WTEYMAKYDI EEVHGSGIRV DLGEDAEVAG TQYRLPSGKC PVFGKGIIIE N SNTTFLTP VATGNQYLKD GGFAFPPTEP LMSPMTLDEM RHFYKDNKYV KNLDELTLCS RHAGNMIPDN DKNSNYKYPA VY DDKDKKC HILYIAAQEN NGPRYCNKDE SKRNSMFCFR PAKDISFQNY TYLSKNVVDN WEKVCPRKNL QNAKFGLWVD GNC EDIPHV NEFPAIDLFE CNKLVFELSA SDQPKQYEQH LTDYEKIKEG FKNKNASMIK SAFLPTGAFK ADRYKSHGKG YNWG NYNTE TQKCEIFNVK PTCLINNSSY IATTALSHPI EVENNFPCSL YKDEIMKEIE RESKRIKLND NDDEGNKKII APRIF ISDD KDSLKCPCDP EMVSNSTCRF FVCKCVERRA EVTSNNEVVV KEEYKDEYAD IPEHKPTYDK MKIIIASSAA VAVLAT ILM VYLYKRKGNA EKYDKMDEPQ DYGKSNSRND EMLDPEASFW GEEKRASHTT PVLMEKPYY

UniProtKB: Apical membrane antigen 1

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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

BufferpH: 7
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 209157
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9ygj:
Plasmodium falciparum moving junction staple - PfAMA1, PfRON2, PfRON4, PfRON5

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