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- PDB-9ygj: Plasmodium falciparum moving junction staple - PfAMA1, PfRON2, Pf... -

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Basic information

Entry
Database: PDB / ID: 9ygj
TitlePlasmodium falciparum moving junction staple - PfAMA1, PfRON2, PfRON4, PfRON5
Components
  • Apical membrane antigen 1
  • Rhoptry neck protein 2
  • Rhoptry neck protein 4
  • Rhoptry neck protein 5
KeywordsMEMBRANE PROTEIN / Invasion / Plasmodium / Apicomplexa / CryoEM / Endogenous
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHaile, M.T. / Zhen, J. / Ho, C.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhoptry neck protein 2
B: Rhoptry neck protein 4
C: Rhoptry neck protein 5
D: Apical membrane antigen 1


Theoretical massNumber of molelcules
Total (without water)591,5854
Polymers591,5854
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

#1: Protein Rhoptry neck protein 2


Mass: 249801.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum NF54 (eukaryote) / References: UniProt: A0A2I0C357
#2: Protein Rhoptry neck protein 4


Mass: 135755.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum NF54 (eukaryote) / References: UniProt: A0A2I0C0S7
#3: Protein Rhoptry neck protein 5


Mass: 133892.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum NF54 (eukaryote) / References: UniProt: A0A2I0BXF6
#4: Protein Apical membrane antigen 1 / Merozoite surface antigen


Mass: 72135.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum NF54 (eukaryote) / References: UniProt: W7JSP8
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: Plasmodium falciparum moving junction staple with PfAMA1 - PfRON2 - PfRON4 - PfRON5
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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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: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
9PHENIX1.21.2_5419model refinement
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209157 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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