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- EMDB-72265: Cryo-electron microscopy structure of PfRIPR bound to monoclonal ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72265
TitleCryo-electron microscopy structure of PfRIPR bound to monoclonal antibodies RP.093, RP.073 and RP.063
Map data
Sample
  • Complex: A complex of RH5-interacting protein with monoclonal antibodies
    • Protein or peptide: RP.093 Heavy Chain
    • Protein or peptide: RP.093 Light Chain
    • Protein or peptide: RP.073 Heavy Chain
    • Protein or peptide: RP.073 Light Chain
    • Protein or peptide: RP.063 Heavy Chain
    • Protein or peptide: RP.063 Light Chain
    • Protein or peptide: Rh5-interacting protein
KeywordsMalaria / RIPR / Monoclonal antibodies / Vaccine / Invasion complex / Plasmodium falciparum / IMMUNE SYSTEM
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 speciesMus musculus (house mouse) / Plasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsBarrett JR / Ward AB
Funding support United States, 1 items
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 21, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72265.png

Downloads & links

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Map

FileDownload / File: emd_72265.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.1228466 - 1.4922159
Average (Standard dev.)-0.0000086838 (±0.01843263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_72265_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72265_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72265_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A complex of RH5-interacting protein with monoclonal antibodies

EntireName: A complex of RH5-interacting protein with monoclonal antibodies
Components
  • Complex: A complex of RH5-interacting protein with monoclonal antibodies
    • Protein or peptide: RP.093 Heavy Chain
    • Protein or peptide: RP.093 Light Chain
    • Protein or peptide: RP.073 Heavy Chain
    • Protein or peptide: RP.073 Light Chain
    • Protein or peptide: RP.063 Heavy Chain
    • Protein or peptide: RP.063 Light Chain
    • Protein or peptide: Rh5-interacting protein

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Supramolecule #1: A complex of RH5-interacting protein with monoclonal antibodies

SupramoleculeName: A complex of RH5-interacting protein with monoclonal antibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: RP.093 Heavy Chain

MacromoleculeName: RP.093 Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.090556 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQQWGAG LLKPSETLSL TCAVYGGSFS GYYWSWIRQP PGKGLEWIGE INHGGDTNYI PSLKSRVTMS VDTSKNQFSL KLTSVTAAD TAVYYCERGQ YSSSSRWFDP WGQGTLVTV

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Macromolecule #2: RP.093 Light Chain

MacromoleculeName: RP.093 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.409633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYDLTQPPSV SVSPGQTASI TCSGDKLGDK YVCWYQQKPG QSPVLVIHRN SKRPSGTFER FSGSNSGNTA TLTISGTQAM DEADYYCQA WDSRIVVFGG GTKLTVL

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Macromolecule #3: RP.073 Heavy Chain

MacromoleculeName: RP.073 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.722105 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSIS SYYWSWIRQP PGKGLEWIGY IYYNGNTGYN PSLKNRVTIS VDTSKNQFSL KLSSVTAAD TAVYYCARGG GNYSFFDYWG QGTLITV

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Macromolecule #4: RP.073 Light Chain

MacromoleculeName: RP.073 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.522544 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SSELTQDPAV SVALGQTVRI TCQGDSLRSY YANWYQQKPG QAPALVIFGK NNRPSGIPDR FSGSSSGNTA SLTITGAQAE DEADYYCNS RDSSGYHRVF GGGTKLTVL

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Macromolecule #5: RP.063 Heavy Chain

MacromoleculeName: RP.063 Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.013626 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLQLQESGPG LVKPSETLSL TCTVSGGSIS SSSYYWGWIR QPPGKGLEWI GNILYSGSTY YNPSLKSRVT ISVDTSKNQL SLKLSSVTA ADTAVYYCAR GFVRGVIGYF QHWGQGTLVT V

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Macromolecule #6: RP.063 Light Chain

MacromoleculeName: RP.063 Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.593729 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVSPGQTARI TCSGDALPKK YAYWYQQKSG QAPVLVIYED SKRPSGIPER FSGSSSGTMA TLTISGAQVE DEADYYCYS TDSSGSHWVF GGGTKLTVL

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Macromolecule #7: Rh5-interacting protein

MacromoleculeName: Rh5-interacting protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 124.275094 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: DLIEGIFYEK NEIDKLTFSL DHRVRDNLKT DLILNNNGEN DYAYLNKYVY TILNRDSTEK IKTFFSHNKD MKSCDYFISK EYQSSDKTN QICYKKTFCG VVIPNSEEIK TNKITNDKLY CAHFQSTHII IYYISQPLLL EPHVVYEETF FEKGKNDQIN C QGMYISLR ...String:
DLIEGIFYEK NEIDKLTFSL DHRVRDNLKT DLILNNNGEN DYAYLNKYVY TILNRDSTEK IKTFFSHNKD MKSCDYFISK EYQSSDKTN QICYKKTFCG VVIPNSEEIK TNKITNDKLY CAHFQSTHII IYYISQPLLL EPHVVYEETF FEKGKNDQIN C QGMYISLR SVHVHTHNAI LQQETLTYIK NLCDGKNNCK FDFDSIKYEQ KSLTHYLFFI NIQYQCISPL NLQENEMCDV YN DDTHKAT CKYGFNKIEL LKNVCEENYR CTQDICSVNQ FCDGENETCT CKTSLLPSAK NNCEYNDLCT VLNCPEQSTC EQI GNGKKA ECKCENGKYY HNNKCYTKND LELAIKIEPH KKEKFYKNNL YQGKALKPEY IFMQCENGFS IEVINAYVSC YRVS FNLNK LKYVTESLKK MCDGKTKCAY GNTIDPIDDL NHHNICNNFN TIFKYDYLCV FNNQQITSDK NSHLHSNIPS LYQSS ILPD IQKSKFHLIS RNSRTNQYPH NQISMLEIQN EISSHNSNQF STDPHTNSNN INNMNIKKVE IFRSRFSSKL QCQGGK INI DKAILKGGEG CNDLLLTNSL KSYCNDLSEC DIGLIYHFDT YCINDQYLFV SYSCSNLCNK CHQQSTCYGN RFNYDCF CD NPYISKYGNK LCERPNDCES VLCSQNQVCQ ILPNDKLICQ CEEGYKNVKG KCVPDNKCDL SCPSNKVCVI ENGKQTCK C SERFVLENGV CICANDYKME DGINCIAKNK CKRKEYENIC TNPNEMCAYN EETDIVKCEC KEHYYRSSRG ECILNDYCK DINCKENEEC SIVNFKPECV CKENLKKNNK GECIYENSCL INEGNCPKDS KCIYREYKPH ECVCNKQGHV AVNGKCVLED KCVHNKKCS ENSICVNVMN KEPICVCTYN YYKKDGVCLI QNPCLKDNGG CSRNSECTFK YSKIQCTCKE NYKNKDDSCV P NTNEYDES FTFQYNDDAS IILGACGMIE FSYIYNQIIW KIQNSKESYV FYYDYPTAGN IEVQIKNEIF HTIIYLKKKI GN SVIYDDF QVDHQTCIYE NVFYYSNQNE PEA

UniProtKB: Rh5-interacting protein

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 259584
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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