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- EMDB-11156: Plasmodium falciparum merozoite surface protein 1 dimer, conforma... -

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Basic information

Entry
Database: EMDB / ID: EMD-11156
TitlePlasmodium falciparum merozoite surface protein 1 dimer, conformation 1
Map dataDimer, C2 reconstruction, unfiltered
Sample
  • Complex: Merozoite surface protein 1 (MSP-1)
    • Protein or peptide: Precursor of the major merozoite surface antigens
    • Protein or peptide: Merozoite surface protein-1
Function / homologyMerozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / membrane => GO:0016020 / plasma membrane / Merozoite surface protein 1 / Merozoite surface protein 1
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.247
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.247
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zbj
  • Surface level: 0.247
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11156.png

Downloads & links

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Map

FileDownload / File: emd_11156.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDimer, C2 reconstruction, unfiltered
Voxel sizeX=Y=Z: 1.077 Å
Density
Contour LevelBy AUTHOR: 0.247 / Movie #1: 0.247
Minimum - Maximum-0.51117456 - 1.53203
Average (Standard dev.)0.0018813235 (±0.04693796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 310.176 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0771.0771.077
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z310.176310.176310.176
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.5111.5320.002

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Supplemental data

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Mask #1

Fileemd_11156_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: Dimer, C2 reconstruction, sharpened

Fileemd_11156_additional_1.map
AnnotationDimer, C2 reconstruction, sharpened
Projections & Slices
AxesZYX

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Additional map: C2 symmetry expansion, C1 monomer reconstruction, unfiltered

Fileemd_11156_additional_2.map
AnnotationC2 symmetry expansion, C1 monomer reconstruction, unfiltered
Projections & Slices
AxesZYX

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Additional map: C2 symmetry expansion, C1 monomer reconstruction, globally sharpened

Fileemd_11156_additional_3.map
AnnotationC2 symmetry expansion, C1 monomer reconstruction, globally sharpened
Projections & Slices
AxesZYX

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Additional map: C2 symmetry expansion, C1 monomer reconstruction, half map 2

Fileemd_11156_additional_4.map
AnnotationC2 symmetry expansion, C1 monomer reconstruction, half map 2
Projections & Slices
AxesZYX

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Additional map: C2 symmetry expansion, C1 monomer reconstruction, half map 1

Fileemd_11156_additional_5.map
AnnotationC2 symmetry expansion, C1 monomer reconstruction, half map 1
Projections & Slices
AxesZYX

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Histogram

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Half map: C2 dimer, half map 1

Fileemd_11156_half_map_1.map
AnnotationC2 dimer, half map 1
Projections & Slices
AxesZYX

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Half map: C2 dimer, half map 2

Fileemd_11156_half_map_2.map
AnnotationC2 dimer, half map 2
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AxesZYX

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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: Precursor of the major merozoite surface antigens
    • 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 (dimer).
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Precursor of the major merozoite surface antigens

MacromoleculeName: Precursor of the major merozoite surface antigens / type: protein_or_peptide / ID: 1
Details: Fusion of the p83 and p30 subunits of the Merozoite surface protein-1 complex
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 101.973172 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 STHTLSQS G ETEVTEETEE TEETVGHTTT VTITLPPTQP SPPKEVKVVE NSIEQKSNDN SQALTKTVYL KKLDEFLTKS YICHKYILV SNSSMDQKLL EVYNLTPEEE NELKSCDPLD LLFNIQNNIP AMYSLYDSMN NDLQHLFFEL YQKEMIYYLH KLKEENHIKK LLEEQKQIT GT

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Macromolecule #2: Merozoite surface protein-1

MacromoleculeName: Merozoite surface protein-1 / type: protein_or_peptide / ID: 2
Details: Fusion of the p38 and p42 subunits of the Merozoite surface protein-1 complex
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 89.615805 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 EAISVTMDNI LSGFENEYDV IYLKPLAGVY RSLKKQIEKN IFTFNLNLND ILNSRLKKRK YFLDV LESD LMQFKHISSN EYIIEDSFKL LNSEQKNTLL KSYKYIKESV ENDIKFAQEG ISYYEKVLAK YKDDLESIKK VIKEEK EKF PSSPPTTPPS PAKTDEQKKE SKFLPFLTNI ETLYNNLVNK IDDYLINLKA KINDCNVEKD EAHVKITKLS DLKAIDD KI DLFKNPYDFE AIKKLINDDT KKDMLGKLLS TGLVQNFPNT IISKLIEGKF QDMLNISQHQ CVKKQCPENS GCFRHLDE R EECKCLLNYK QEGDKCVENP NPTCNENNGG CDADATCTEE DSGSSRKKIT CECTKPDSYP LFDGIFCSSS N

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: OTHER / Details: Ab initio model generated from the data
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 271763
FSC plot (resolution estimation)

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