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- EMDB-56281: PfRIPR bound to monoclonal antibody MAD8-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-56281
TitlePfRIPR bound to monoclonal antibody MAD8-2
Map dataprimary map
Sample
  • Complex: PfRIPR bound to monoclonal MAD8-2
    • Protein or peptide: Rh5-interacting protein
    • Protein or peptide: MAD8-2 heavy chain
    • Protein or peptide: MAD8-2 light chain
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 / 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) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56281.png

Downloads & links

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Map

FileDownload / File: emd_56281.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 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: 0.0016
Minimum - Maximum-0.013751261 - 0.02018037
Average (Standard dev.)-0.000004342622 (±0.00037602597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56281_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_56281_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_56281_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_56281_half_map_2.map
Annotationhalf map B
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 bound to monoclonal MAD8-2

EntireName: PfRIPR bound to monoclonal MAD8-2
Components
  • Complex: PfRIPR bound to monoclonal MAD8-2
    • Protein or peptide: Rh5-interacting protein
    • Protein or peptide: MAD8-2 heavy chain
    • Protein or peptide: MAD8-2 light chain

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Supramolecule #1: PfRIPR bound to monoclonal MAD8-2

SupramoleculeName: PfRIPR bound to monoclonal 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: 128.313844 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 FCDGEQETCT 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: MAD8-2 heavy chain

MacromoleculeName: MAD8-2 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.554984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE VQLVEFGGGL VQPGGSLRLS CEGSGFIFSQ YWMSWIRQAP GKGLEWVGNI KQDGTEKNYV DSVKGRFTI SRDNTNNFLY LQMDSLRAED TGVYFCARNT FYFDSSGYPL GQGALVAVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV ...String:
MGWSCIILFL VATATGVHSE VQLVEFGGGL VQPGGSLRLS CEGSGFIFSQ YWMSWIRQAP GKGLEWVGNI KQDGTEKNYV DSVKGRFTI SRDNTNNFLY LQMDSLRAED TGVYFCARNT FYFDSSGYPL GQGALVAVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PK SCDKTHT CGKHHHHHH

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Macromolecule #3: MAD8-2 light chain

MacromoleculeName: MAD8-2 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.321291 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSA IQMTQSPSTL SASVGDSVTI SCRASQSISS WLAWYQQKPG KAPNLLIYKA SILESGVPSR FSGSGSGTE FTLTISSLQP DDFATYYCQK YDSYPYSFGP GTKLDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MGWSCIILFL VATATGVHSA IQMTQSPSTL SASVGDSVTI SCRASQSISS WLAWYQQKPG KAPNLLIYKA SILESGVPSR FSGSGSGTE FTLTISSLQP DDFATYYCQK YDSYPYSFGP GTKLDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 191422
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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