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- PDB-9q7c: Cryo-electron microscopy structure of PfRIPR bound to monoclonal ... -

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Basic information

Entry
Database: PDB / ID: 9q7c
TitleCryo-electron microscopy structure of PfRIPR bound to monoclonal antibodies RP.092 and RP.052
Components
  • RP.052 Heavy Chain
  • RP.052 Light Chain
  • RP.092 Heavy Chain
  • RP.092 Light Chain
  • Rh5-interacting protein
KeywordsIMMUNE SYSTEM / Malaria / RIPR / Monoclonal antibodies / Vaccine / Invasion complex / Plasmodium falciparum
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / host cell membrane / cytoplasmic vesicle / host extracellular region / host cell plasma membrane / protein-containing complex / extracellular region / membrane / plasma membrane
Similarity search - Function
Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Rh5-interacting protein
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.01 Å
AuthorsBarrett, J.R. / Ward, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Immunity / Year: 2026
Title: Analysis of monoclonal antibodies against the malaria invasion complex protein RIPR reveals the structural basis for synergistic antibody protection.
Authors: Barnabas G Williams / Jordan R Barrett / Josefin Bartholdson Scott / Cassandra A Rigby / Matteo Cagiada / Doris Quinkert / Kirsty McHugh / Anna Huhn / Sean A Burnap / Camille Gourjault / ...Authors: Barnabas G Williams / Jordan R Barrett / Josefin Bartholdson Scott / Cassandra A Rigby / Matteo Cagiada / Doris Quinkert / Kirsty McHugh / Anna Huhn / Sean A Burnap / Camille Gourjault / Francesca Byrne / Sai Sundar Rajan Raghavan / Ana Rodrigues / Laura Bergamaschi / Beatrice Balzarotti / Simon Watson / Noah Miller / Lloyd D W King / Francesca R Donnellan / Camilla A Gladstone / Jemima Paterson / Stefania Scalabrino / Sarah E Silk / Jo Salkeld / Angela M Minassian / Katherine Skinner / Weston B Struwe / Charlotte M Deane / Stephen T Reece / Andrew B Ward / Simon J Draper /
Abstract: Plasmodium falciparum RH5-interacting protein (RIPR) is central to the essential PTRAMP-CSS-RIPR-CyRPA-RH5 (PCRCR) complex, a leading target of blood-stage malaria vaccines. However, mechanisms ...Plasmodium falciparum RH5-interacting protein (RIPR) is central to the essential PTRAMP-CSS-RIPR-CyRPA-RH5 (PCRCR) complex, a leading target of blood-stage malaria vaccines. However, mechanisms whereby anti-RIPR antibodies inhibit parasite invasion are poorly understood. We characterized 83 human IgG monoclonal antibodies (mAbs) from RIPR-vaccinated Kymouse platform mice. Single mAbs had minimal neutralizing activity; however, high-level synergistic inhibition was observed with pools of mAbs targeting the RIPR-tail region. Structural characterization and molecular dynamics simulations of RIPR-tail showed that mAbs targeting epidermal growth factor (EGF)-like domains 6-8 (RIPR), but not RIPR or the C-terminal domain (RIPR), synergized to constrain the RIPR-tail conformation. The same antibodies dissociated PTRAMP-CSS from RIPR, thereby enabling anti-RIPR mAbs or anti-CSS single-domain Abs to bind and potentiate anti-RIPR IgG. Addition of these mAbs to IgG from humans immunized with the R78C (RIPR-CyRPA) candidate vaccine enhanced malaria growth inhibition. These data provide a framework to guide next-generation blood-stage malaria vaccine design.
History
DepositionAug 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rh5-interacting protein
B: RP.092 Heavy Chain
C: RP.092 Light Chain
D: RP.052 Heavy Chain
E: RP.052 Light Chain


Theoretical massNumber of molelcules
Total (without water)172,3785
Polymers172,3785
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 Rh5-interacting protein / PfRipr


Mass: 124275.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: RIPR, PFC1045C, PF3D7_0323400 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: O97302
#2: Protein RP.092 Heavy Chain


Mass: 12242.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody RP.092 Light Chain


Mass: 11439.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Antibody RP.052 Heavy Chain


Mass: 12797.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#5: Antibody RP.052 Light Chain


Mass: 11622.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
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: A complex of RH5-interacting protein with monoclonal antibodies
Type: COMPLEX / Entity ID: #2-#5, #1 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143032 / Symmetry type: POINT
RefinementHighest resolution: 4.01 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034111
ELECTRON MICROSCOPYf_angle_d0.7335563
ELECTRON MICROSCOPYf_dihedral_angle_d13.0461486
ELECTRON MICROSCOPYf_chiral_restr0.046605
ELECTRON MICROSCOPYf_plane_restr0.007721

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