[English] 日本語
Yorodumi
- EMDB-11153: Merozoite surface protein 1 (MSP-1) from Plasmodium falciparum, a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11153
TitleMerozoite surface protein 1 (MSP-1) from Plasmodium falciparum, alternative conformation 3
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 1Merozoite surface protein
Function / homologyMerozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / plasma membrane / Merozoite surface protein 1 / Merozoite surface protein 1 / 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: 3.2 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

-
Structure visualization

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

emd_11153.png

Downloads & links

-
Map

FileDownload / File: emd_11153.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Voxel sizeX=Y=Z: 1.073 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.8353619 - 1.7107148
Average (Standard dev.)-0.0016040129 (±0.040710237)
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-0.8351.711-0.002

-
Supplemental data

-
Mask #1

Fileemd_11153_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map

Fileemd_11153_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_11153_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11153_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 1Merozoite surface protein

-
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)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE / Details: Ab initio model generated from the data
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 124774
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more