[English] 日本語
Yorodumi
- PDB-6zbe: Merozoite surface protein 1 (MSP-1) from Plasmodium falciparum, a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zbe
TitleMerozoite surface protein 1 (MSP-1) from Plasmodium falciparum, alternative conformation 1
Components
  • (Merozoite surface antigens) x 2
  • Merozoite surface protein 1
  • Merozoite surface protein-1
KeywordsMEMBRANE PROTEIN / Merozoite surface protein 1 / malaria / Plasmodium falciparum / MSP-1 / p190 / GPI-anchored 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)
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 1.2Nov 13, 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11152
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Merozoite surface antigens
B: Merozoite surface antigens
C: Merozoite surface protein-1
D: Merozoite surface protein 1


Theoretical massNumber of molelcules
Total (without water)191,6254
Polymers191,6254
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18950 Å2
ΔGint-167 kcal/mol
Surface area64560 Å2
MethodPISA

-
Components

#1: Protein Merozoite surface antigens / Merozoite surface protein 1 / PMMSA


Mass: 81773.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Subunit of the MSP-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 antigens / Merozoite surface protein 1 / PMMSA


Mass: 20217.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Subunit of the MSP-1 complex
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: msp1 / Production host: Escherichia coli (E. coli) / References: UniProt: M1V901
#3: Protein Merozoite surface protein-1


Mass: 46390.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Subunit of the MSP-1 complex
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: msp1 / Production host: Escherichia coli (E. coli) / References: UniProt: M1VNZ6
#4: Protein Merozoite surface protein 1


Mass: 43243.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Subunit of the MSP-1 complex
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: msp1 / Production host: Escherichia coli (E. coli) / References: UniProt: C4PDY5
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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 (monomer), processed with SUB-1 protease into the MSP-1 complex composed of the subunits p83, p30, p38, and p42
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
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
VitrificationCryogen name: ETHANE

-
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: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

-
Processing

EM softwareName: cryoSPARC / Version: 2.5 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112939 / Symmetry type: POINT

+
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