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- PDB-6zbj: Plasmodium falciparum merozoite surface protein 1 dimer, conforma... -

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Basic information

Entry
Database: PDB / ID: 6zbj
TitlePlasmodium falciparum merozoite surface protein 1 dimer, conformation 1
Components
  • Merozoite surface protein-1
  • Precursor of the major merozoite surface antigens
KeywordsMEMBRANE PROTEIN / Merozoite surface protein 1 / malaria / Plasmodium falciparum / MSP-1 / p190 / GPI-anchored membrane protein
Function / homologyMerozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / vacuolar membrane / extracellular region / plasma membrane / Merozoite surface protein 1 / Merozoite surface protein 1
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDijkman, P.M. / Kudryashev, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt FoundationSofja Kovalevskaja Award to Mikhail Kudryashev Germany
Citation
Journal: Sci Adv / Year: 2021
Title: Structure of the merozoite surface protein 1 from .
Authors: Patricia M Dijkman / Tanja Marzluf / Yingyi Zhang / Shih-Ying Scott Chang / Dominic Helm / Michael Lanzer / Hermann Bujard / Mikhail Kudryashev /
Abstract: The merozoite surface protein 1 (MSP-1) is the most abundant protein on the surface of the erythrocyte-invading merozoite, the causative agent of malaria. MSP-1 is essential for merozoite formation, ...The merozoite surface protein 1 (MSP-1) is the most abundant protein on the surface of the erythrocyte-invading merozoite, the causative agent of malaria. MSP-1 is essential for merozoite formation, entry into and escape from erythrocytes, and is a promising vaccine candidate. Here, we present monomeric and dimeric structures of full-length MSP-1. MSP-1 adopts an unusual fold with a large central cavity. Its fold includes several coiled-coils and shows structural homology to proteins associated with membrane and cytoskeleton interactions. MSP-1 formed dimers through these domains in a concentration-dependent manner. Dimerization is affected by the presence of the erythrocyte cytoskeleton protein spectrin, which may compete for the dimerization interface. Our work provides structural insights into the possible mode of interaction of MSP-1 with erythrocytes and establishes a framework for future investigations into the role of MSP-1 in infection and immunity.
#1: Journal: Sci Adv / Year: 2021
Title: Structure of the merozoite surface protein 1 from Plasmodium falciparum
Authors: Dijkman, P.M. / Marzluf, T. / Zhang, Y. / Chang, S.Y.S. / Helm, D. / Lanzer, M. / Bujard, H. / Kudryashev, M.
History
DepositionJun 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Precursor of the major merozoite surface antigens
B: Merozoite surface protein-1
C: Precursor of the major merozoite surface antigens
D: Merozoite surface protein-1


Theoretical massNumber of molelcules
Total (without water)383,1784
Polymers383,1784
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimerisation further supported by microscale thermophoresis (MST).
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24290 Å2
ΔGint-194 kcal/mol
Surface area127870 Å2
MethodPISA

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Components

#1: Protein Precursor of the major merozoite surface antigens


Mass: 101973.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion of the p83 and p30 subunits of the Merozoite surface protein-1 complex
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: gp190/ MSA1/ MSP1/ PMMSA / Production host: Escherichia coli (E. coli) / References: UniProt: Q25922
#2: Protein Merozoite surface protein-1


Mass: 89615.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion of the p38 and p42 subunits of the Merozoite surface protein-1 complex
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: msp1 / Production host: Escherichia coli (E. coli) / References: UniProt: M1VF06
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: Merozoite surface protein 1 (MSP-1) / Type: COMPLEX
Details: Heteromeric assembly of p83/30 fusion and p38/42 fusion of MSP-1 from Plasmodium falciparum (dimer).
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Source (recombinant)Organism: Escherichia coli (E. coli)
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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
13cryoSPARC2.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271763 / Symmetry type: POINT

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