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- EMDB-11150: Merozoite surface protein 1 (MSP-1) from Plasmodium falciparum, m... -

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Basic information

Entry
Database: EMDB / ID: EMD-11150
TitleMerozoite surface protein 1 (MSP-1) from Plasmodium falciparum, main conformation
Map dataUnfiltered map
Sample
  • Complex: Merozoite surface protein 1 (MSP-1)
    • Protein or peptide: Merozoite surface antigens
    • Protein or peptide: Merozoite surface antigens
    • Protein or peptide: Merozoite surface protein-1
    • Protein or peptide: Merozoite surface protein 1
KeywordsMerozoite surface protein 1 / malaria / Plasmodium falciparum / MSP-1 / p190 / GPI-anchored membrane protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


vacuolar membrane / extracellular region / plasma membrane
Similarity search - Function
Merozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1
Similarity search - Domain/homology
Merozoite surface protein 1 / Merozoite surface protein 1 / Merozoite surface protein 1 / Merozoite surface protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDijkman PM / Kudryashev M
Funding support Germany, 1 items
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 PM / Marzluf T / Zhang Y / Chang SYS / Helm D / Lanzer M / Bujard H / Kudryashev M
History
DepositionJun 8, 2020-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zbc
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11150.png

Downloads & links

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Map

FileDownload / File: emd_11150.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 288 pix.
= 309.024 Å		1.07 Å/pix.
x 288 pix.
= 309.024 Å		1.07 Å/pix.
x 288 pix.
= 309.024 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.073 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.7927739 - 1.9422606
Average (Standard dev.)-0.001838528 (±0.043921802)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 309.024 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z309.024309.024309.024
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.7931.942-0.002

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Supplemental data

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Mask #1

Fileemd_11150_msk_1.map
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Additional map: Sharpened map

Fileemd_11150_additional_1.map
AnnotationSharpened map
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Additional map: Focused refinement coiled-coil domain, unfiltered

Fileemd_11150_additional_2.map
AnnotationFocused refinement coiled-coil domain, unfiltered
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Additional map: Focused refinement wing domain, sharpened

Fileemd_11150_additional_3.map
AnnotationFocused refinement wing domain, sharpened
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Additional map: Focused refinement wing domain, unfiltered

Fileemd_11150_additional_4.map
AnnotationFocused refinement wing domain, unfiltered
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Additional map: Focused refinement coiled-coil domain, sharpened

Fileemd_11150_additional_5.map
AnnotationFocused refinement coiled-coil domain, sharpened
Projections & Slices
AxesZYX

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Additional map: Sharpened map (DeepEMhancer)

Fileemd_11150_additional_6.map
AnnotationSharpened map (DeepEMhancer)
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AxesZYX

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Additional map: Focused refinement wing domain, sharpened (DeepEMhancer)

Fileemd_11150_additional_7.map
AnnotationFocused refinement wing domain, sharpened (DeepEMhancer)
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_11150_half_map_1.map
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Half map: #1

Fileemd_11150_half_map_2.map
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Sample components

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Entire : Merozoite surface protein 1 (MSP-1)

EntireName: Merozoite surface protein 1 (MSP-1)
Components
  • Complex: Merozoite surface protein 1 (MSP-1)
    • Protein or peptide: Merozoite surface antigens
    • Protein or peptide: Merozoite surface antigens
    • Protein or peptide: Merozoite surface protein-1
    • Protein or peptide: Merozoite surface protein 1

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Supramolecule #1: Merozoite surface protein 1 (MSP-1)

SupramoleculeName: Merozoite surface protein 1 (MSP-1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Heteromeric assembly of p83/30 fusion and p38/42 fusion of MSP-1 from Plasmodium falciparum (monomer), processed with SUB-1 protease into the MSP-1 complex composed of the subunits p83, p30, p38, and p42
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: Merozoite surface antigens

MacromoleculeName: Merozoite surface antigens / type: protein_or_peptide / ID: 1 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 81.773539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VTHESYQELV KKLEALEDAV LTGYSLFQKE KMVLNEEEIT TKGASAQSGA SAQSGASAQS GASAQSGASA QSGASAQSGT SGPSGPSGT SPSSRSNTLP RSNTSSGASP PADASDSDAK SYADLKHRVR NYLFTIKELK YPELFDLTNH MLTLCDNIHG F KYLIDGYE ...String:
VTHESYQELV KKLEALEDAV LTGYSLFQKE KMVLNEEEIT TKGASAQSGA SAQSGASAQS GASAQSGASA QSGASAQSGT SGPSGPSGT SPSSRSNTLP RSNTSSGASP PADASDSDAK SYADLKHRVR NYLFTIKELK YPELFDLTNH MLTLCDNIHG F KYLIDGYE EINELLYKLN FYFDLLRAKL NDVCANDYCQ IPFNLKIRAN ELDVLKKLVF GYRKPLDNIK DNVGKMEDYI KK NKTTIAN INELIEGSKK TIDQNKNADN EEGKKKLYQA QYDLSIYNKQ LEEAHNLISV LEKRIDTLKK NENIKKLLDK INE IKNPPP ANSGNTPNTL LDKNKKIEEH EEKIKEIAKT IKFNIDSLFT DPLELEYYLR EKNKKVDVTP KSQDPTKSVQ IPKV PYPNG IVYPLPLTDI HNSLAADNDK NSYGDLMNPH TKEKINEKII TDNKERKIFI NNIKKKIDLE EKNINHTKEQ NKKLL EDYE KSKKDYEELL EKFYEMKFNN NFDKDVVDKI FSARYTYNVE KQRYNNKFSS SNNSVYNVQK LKKALSYLED YSLRKG ISE KDFNHYYTLK TGLEADIKKL TEEIKSSENK ILEKNFKGLT HSANGSLEVS DIVKLQVQKV LLIKKIEDLR KIELFLK NA QLKDSIHVPN IYKPQNKPEP YYLIVLKKEV DKLKEFIPKV KDMLKKEQAV LSSITQPLVA ASETTEDGGH STHTL

UniProtKB: Merozoite surface protein 1

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Macromolecule #2: Merozoite surface antigens

MacromoleculeName: Merozoite surface antigens / type: protein_or_peptide / ID: 2 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 20.217637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SQSGETEVTE ETEETEETVG HTTTVTITLP PTQPSPPKEV KVVENSIEQK SNDNSQALTK TVYLKKLDEF LTKSYICHKY ILVSNSSMD QKLLEVYNLT PEEENELKSC DPLDLLFNIQ NNIPAMYSLY DSMNNDLQHL FFELYQKEMI YYLHKLKEEN H IKKLLEEQ KQITGT

UniProtKB: Merozoite surface protein 1

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Macromolecule #3: Merozoite surface protein-1

MacromoleculeName: Merozoite surface protein-1 / type: protein_or_peptide / ID: 3 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 46.390676 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SSTSSPGNTT VNTAQSATHS NSQNQQSNAS STNTQNGVAV SSGPAVVEES HDPLTVLSIS NDLKGIVSLL NLGNKTKVPN PLTISTTEM EKFYENILKN NDTYFNDDIK QFVKSNSKVI TGLTETQKNA LNDEIKKLKD TLQLSFDLYN KYKLKLDRLF N KKKELGQD ...String:
SSTSSPGNTT VNTAQSATHS NSQNQQSNAS STNTQNGVAV SSGPAVVEES HDPLTVLSIS NDLKGIVSLL NLGNKTKVPN PLTISTTEM EKFYENILKN NDTYFNDDIK QFVKSNSKVI TGLTETQKNA LNDEIKKLKD TLQLSFDLYN KYKLKLDRLF N KKKELGQD KMQIKKLTLL KEQLESKLNS LNNPHNVLQN FSVFFNKKKE AEIAETENTL ENTKILLKHY KGLVKYYNGE SS PLKTLSE VSIQTEDNYA NLEKFRVLSK IDGKLNDNLH LGKKKLSFLS SGLHHLITEL KEVIKNKNYT GNSPSENNKK VNE ALKSYE NFLPEAKVTT VVTPPQPDVT PSPLSVRVSG SSGSTKEETQ IPTSGSLLTE LQQVVQLQNY DEEDDSLVVL PIFG ESEDN DEYLDQVVTG E

UniProtKB: Merozoite surface protein 1

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Macromolecule #4: Merozoite surface protein 1

MacromoleculeName: Merozoite surface protein 1 / type: protein_or_peptide / ID: 4 / Details: Subunit of the MSP-1 complex / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 43.243133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AISVTMDNIL SGFENEYDVI YLKPLAGVYR SLKKQIEKNI FTFNLNLNDI LNSRLKKRKY FLDVLESDLM QFKHISSNEY IIEDSFKLL NSEQKNTLLK SYKYIKESVE NDIKFAQEGI SYYEKVLAKY KDDLESIKKV IKEEKEKFPS SPPTTPPSPA K TDEQKKES ...String:
AISVTMDNIL SGFENEYDVI YLKPLAGVYR SLKKQIEKNI FTFNLNLNDI LNSRLKKRKY FLDVLESDLM QFKHISSNEY IIEDSFKLL NSEQKNTLLK SYKYIKESVE NDIKFAQEGI SYYEKVLAKY KDDLESIKKV IKEEKEKFPS SPPTTPPSPA K TDEQKKES KFLPFLTNIE TLYNNLVNKI DDYLINLKAK INDCNVEKDE AHVKITKLSD LKAIDDKIDL FKNPYDFEAI KK LINDDTK KDMLGKLLST GLVQNFPNTI ISKLIEGKFQ DMLNISQHQC VKKQCPENSG CFRHLDEREE CKCLLNYKQE GDK CVENPN PTCNENNGGC DADATCTEED SGSSRKKITC ECTKPDSYPL FDGIFCSSSN

UniProtKB: Merozoite surface protein 1

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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
DetailsHeteromeric assembly of p83/30 fusion and p38/42 fusion of MSP-1 from Plasmodium falciparum (monomer), processed with SUB-1 protease into the MSP-1 complex composed of the subunits p83, p30, p38, and p42

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio model generated from the data
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 141838
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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