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- EMDB-56282: PfRIPR and PfCyRPA -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56282
TitlePfRIPR and PfCyRPA
Map data
Sample
  • Complex: PfRIPR, PfCyPRA, Cy.007 and MAD8-2
    • Protein or peptide: Rh5-interacting protein
    • Protein or peptide: Cysteine-rich protective antigen
KeywordsMalaria / antibody / vaccine design / erythrocyte invasion / Plasmodium falciparum / PfRIPR / PfPCRCR / CELL ADHESION
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / host cell membrane / apical part of cell / cytoplasmic vesicle / host extracellular region / host cell plasma membrane / protein-containing complex / extracellular region ...microneme lumen / microneme / symbiont entry into host / host cell membrane / apical part of cell / cytoplasmic vesicle / host extracellular region / host cell plasma membrane / protein-containing complex / extracellular region / membrane / plasma membrane
Similarity search - Function
Cysteine-rich protective antigen 6 bladed domain / Cysteine-Rich Protective Antigen 6 bladed domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Rh5-interacting protein / Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsFarrell B / Higgins MK
Funding support United Kingdom, United States, 2 items
OrganizationGrant numberCountry
Wellcome Trust220797/Z/20/Z United Kingdom
Bill & Melinda Gates FoundationINV-076909 United States
CitationJournal: To Be Published
Title: Dynamic hinge-motion of PfRIPR revealed by malaria invasion inhibitory antibodies
Authors: Farrell B / Higgins MK
History
DepositionJan 10, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56282.png

Downloads & links

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Map

FileDownload / File: emd_56282.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 366.08 Å		0.83 Å/pix.
x 440 pix.
= 366.08 Å		0.83 Å/pix.
x 440 pix.
= 366.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.11369354 - 0.26397294
Average (Standard dev.)-0.0001458904 (±0.0033197422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 366.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56282_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_56282_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map

Fileemd_56282_additional_2.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_56282_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_56282_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PfRIPR, PfCyPRA, Cy.007 and MAD8-2

EntireName: PfRIPR, PfCyPRA, Cy.007 and MAD8-2
Components
  • Complex: PfRIPR, PfCyPRA, Cy.007 and MAD8-2
    • Protein or peptide: Rh5-interacting protein
    • Protein or peptide: Cysteine-rich protective antigen

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Supramolecule #1: PfRIPR, PfCyPRA, Cy.007 and MAD8-2

SupramoleculeName: PfRIPR, PfCyPRA, Cy.007 and MAD8-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Macromolecule #1: Rh5-interacting protein

MacromoleculeName: Rh5-interacting protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 128.299812 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MKLCILLAVV AFVGLSLGGT DLIEGIFYEK NEIDKLTFSL DHRVRDNLKT DLILNNNGEN DYAYLNKYVY TILNRDSTEK IKTFFSHNK DMKSCDYFIS KEYQSSDKTN QICYKKTFCG VVIPNSEEIK TNKITNDKLY CAHFQSTHII IYYISQPLLL E PHVVYEET ...String:
MKLCILLAVV AFVGLSLGGT DLIEGIFYEK NEIDKLTFSL DHRVRDNLKT DLILNNNGEN DYAYLNKYVY TILNRDSTEK IKTFFSHNK DMKSCDYFIS KEYQSSDKTN QICYKKTFCG VVIPNSEEIK TNKITNDKLY CAHFQSTHII IYYISQPLLL E PHVVYEET FFEKGKNDQI NCQGMYISLR SVHVHTHNAI LQQETLTYIK NLCDGKNNCK FDFDSIKYEQ KSLTHYLFFI NI QYQCISP LNLQENEMCD VYNDDTHKAT CKYGFNKIEL LKNVCEENYR CTQDICSVNQ FCDGENETCT CKTSLLPSAK NNC EYNDLC TVLNCPEQST CEQIGNGKKA ECKCENGKYY HNNKCYTKND LELAIKIEPH KKEKFYKNNL YQGKALKPEY IFMQ CENGF SIEVINAYVS CYRVSFNLNK LKYVTESLKK MCDGKTKCAY GNTIDPIDDL NHHNICNNFN TIFKYDYLCV FNNQQ ITSD KNSHLHSNIP SLYQSSILPD IQKSKFHLIS RNSRTNQYPH NQISMLEIQN EISSHNSNQF STDPHTNSNN INNMNI KKV EIFRSRFSSK LQCQGGKINI DKAILKGGEG CNDLLLTNSL KSYCNDLSEC DIGLIYHFDT YCINDQYLFV SYSCSNL CN KCHQQSTCYG NRFNYDCFCD NPYISKYGNK LCERPNDCES VLCSQNQVCQ ILPNDKLICQ CEEGYKNVKG KCVPDNKC D LSCPSNKVCV IENGKQTCKC SERFVLENGV CICANDYKME DGINCIAKNK CKRKEYENIC TNPNEMCAYN EETDIVKCE CKECYYRSSR GECILNDYCK DINCKENEEC SIVNCKPECV CKENLKKNNK GECIYENSCL INEGNCPKDS KCIYREYKPH ECVCNKQGH VAVNGKCVLE DKCVHNKKCS ENSICVNVMN KEPICVCTYN YYKKDGVCLI QNPCLKDNGG CSRNSECTFK Y SKIQCTCK ENYKNKDDSC VPNTNEYDES FTFQYNDDAS IILGACGMIE FSYIYNQIIW KIQNSKESYV FYYDYPTAGN IE VQIKNEI FHTIIYLKKK IGNSVIYDDF QVDHQTCIYE NVFYYSNQNG SASGLNDIFE AQKIEWHEEP EA

UniProtKB: Rh5-interacting protein

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Macromolecule #2: Cysteine-rich protective antigen

MacromoleculeName: Cysteine-rich protective antigen / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 40.184039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DSRHVFIRTE LSFIKNNVPC IRDMFFIYKR ELYNICLDDL KGEEDETHIY VQKKVKDSWI TLNDLFKETD LTGRPHIFAY VDVEEIIIL LCEDEEFSNR KKDMTCHRFY SNDGKEYNNA EITISDYILK DKLLSSYVSL PLKIENREYF LICGVSPYKF K DDNKKDDI ...String:
DSRHVFIRTE LSFIKNNVPC IRDMFFIYKR ELYNICLDDL KGEEDETHIY VQKKVKDSWI TLNDLFKETD LTGRPHIFAY VDVEEIIIL LCEDEEFSNR KKDMTCHRFY SNDGKEYNNA EITISDYILK DKLLSSYVSL PLKIENREYF LICGVSPYKF K DDNKKDDI LCMASHDKGE TWGTKIVIKY DNYKLGVQYF FLRPYISKND LSFHFYVGDN INNVKNVNFI ECTHEKDLEF VC SNRDFLK DNKVLQDVST LNDEYIVSYG NDNNFAECYI FFNNENSILI KPEKYGNTAA GCYGGTFVKI DENRALFIYS SSQ GIYNIH TIYYANYEGG GGSEPEA

UniProtKB: Cysteine-rich protective antigen

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 39.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 205238
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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