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- EMDB-51634: PfMSP3 in complex with mAb MP3.01 -

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Basic information

Entry
Database: EMDB / ID: EMD-51634
TitlePfMSP3 in complex with mAb MP3.01
Map dataPfMSP3 in complex with mAb MP3.01
Sample
  • Complex: PfMSP3 in complex with neutralizing mAb MP3.01
    • Protein or peptide: PfMSP3
KeywordsMalaria / complement regulation / C1-INH / Plasmodium falciparum / MSP3 / neutralizing antibody / IMMUNE SYSTEM
Function / homologyMerozoite surface protein-type / Merozoite surface protein (SPAM) / Merozoite surface protein 3
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBjoernsson KH / Barfod L / Ward AB
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF170C0026778 Denmark
CitationJournal: PLoS Pathog / Year: 2025
Title: Deposition of complement regulators on the surface of Plasmodium falciparum merozoites depends on the immune status of the host.
Authors: Maria Rosaria Bassi / Bogdan Cristinoi / Frank Buitenwerf / Mark Bergholt Cuadrado / Kasper Haldrup Björnsson / Melanie Rose Walker / Frederica Dedo Partey / Andrew B Ward / Michael Fokuo Ofori / Lea Barfod /
Abstract: Plasmodium falciparum is responsible for the majority of malaria cases and deaths worldwide. In malaria endemic areas, natural immunity to blood stage infection is acquired over several exposures to ...Plasmodium falciparum is responsible for the majority of malaria cases and deaths worldwide. In malaria endemic areas, natural immunity to blood stage infection is acquired over several exposures to the parasite and is thought to rely on antibodies. Antibodies can protect from severe disease through different effector functions, with complement activation lately emerging as an important feature of protective humoral responses to malaria. Plasmodium parasites have however evolved several mechanisms to evade complement attack, including the recruitment of complement down-regulatory proteins like Factor H (FH) and C1 esterase inhibitor (C1-INH). In this study, we report that merozoite-specific antibodies acquired naturally after infection activate the complement cascade in an exposure-dependent manner. Using plasma samples from convalescent children and exposed adults collected respectively in Hohoe and Accra (Ghana), we show that the ability to fix C1q and activate the classical pathway is similar for antibodies deriving from the two donors groups. However, downstream complement activation shown as deposition of the membrane attack complex (MAC) is strikingly higher with antibodies from children compared to antibodies from adults. Moreover, we demonstrate that antibodies from naturally exposed children can interfere with the merozoite recruitment of FH, but not of C1-INH. With the aim of neutralizing parasite evasion of the complement classical pathway, we develop a murine monoclonal antibody targeting PfMSP3, the binding partner of C1-INH on the merozoite surface. We demonstrate that this antibody can effectively block the binding of C1-INH to the parasite surface, unlike the naturally acquired ones. Using cryogenic electron microscopy, we obtain a low-resolution structure of the monoclonal antibody in complex with PfMSP3, which is the first reported structural data for this antigen. We propose targeting parasite antigens binding to complement down-regulators, together with leading vaccine candidate antigens, as a novel strategy to enhance the efficacy of future malaria vaccines.
History
DepositionSep 24, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51634.png

Downloads & links

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Map

FileDownload / File: emd_51634.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPfMSP3 in complex with mAb MP3.01
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 320 pix.
= 229.76 Å		0.72 Å/pix.
x 320 pix.
= 229.76 Å		0.72 Å/pix.
x 320 pix.
= 229.76 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: 0.1
Minimum - Maximum-0.50348294 - 0.84338784
Average (Standard dev.)-0.00011162911 (±0.013238527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 229.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: PfMSP3 in complex with mAb MP3.0 - half map A

Fileemd_51634_half_map_1.map
AnnotationPfMSP3 in complex with mAb MP3.0 - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PfMSP3 in complex with mAb MP3.0 - half map B

Fileemd_51634_half_map_2.map
AnnotationPfMSP3 in complex with mAb MP3.0 - half 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 : PfMSP3 in complex with neutralizing mAb MP3.01

EntireName: PfMSP3 in complex with neutralizing mAb MP3.01
Components
  • Complex: PfMSP3 in complex with neutralizing mAb MP3.01
    • Protein or peptide: PfMSP3

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Supramolecule #1: PfMSP3 in complex with neutralizing mAb MP3.01

SupramoleculeName: PfMSP3 in complex with neutralizing mAb MP3.01 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7

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Macromolecule #1: PfMSP3

MacromoleculeName: PfMSP3 / type: protein_or_peptide / ID: 1 / Details: PfMSP3, rat CD4 tag, biotinylation site / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KEIVKKYNLN LRNAILNNNA QIENEENVNT AITGNDFSGG EFLWPGYTEE LKAKKASEDA EKAANDAENA AKEAEEAAKE AVNLKESDKS YTKAKEACTA ASKAKKAVET ALKAKDDAEK SSKADSISTK TKEYAEKAKN AYEKAKNAYQ KANQAVLKAK EASSYDYILG ...String:
KEIVKKYNLN LRNAILNNNA QIENEENVNT AITGNDFSGG EFLWPGYTEE LKAKKASEDA EKAANDAENA AKEAEEAAKE AVNLKESDKS YTKAKEACTA ASKAKKAVET ALKAKDDAEK SSKADSISTK TKEYAEKAKN AYEKAKNAYQ KANQAVLKAK EASSYDYILG WEFGGGVPEH KKEENMLSHL YVSSKDKENI AKENDDVLDE KEEEAEETEE EELEEKNEEE TESEISEDEE EEEEEEEKEE ENDKKKEQEK EQSNENNDQK KDMEAQNLIS KNQNNNEKNV KEAAESIMKT LAGLIKGNNQ IDSTLKDLVE ELSKYFKNHG APSTSITAYK SEGESAEFSF PLNLGEESLQ GELRWKAEKA PSSQSWITFS LKNQKVSVQK STSNPKFQLS ETLPLTLQIP QVSLQFAGSG NLTLTLDRGI LYQEVNLVVM KVTQPDSNTL TCEVMGPTSP KMRLILKQEN QEARVSRQEK VIQVQAPEAG VWQCLLSEGE EVKMDSKIQV LSKGLNSGSL HHILDAQKMV WNHR

UniProtKB: Merozoite surface protein 3

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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

Concentration1.1 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsPfMSP3 complexed with Fab of mAb MP3.01

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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 / Nominal magnification: 195000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 62230673
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 66277
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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