[English] 日本語
Yorodumi
- PDB-7aln: Cryo-EM structure of the divergent actomyosin complex from Plasmo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aln
TitleCryo-EM structure of the divergent actomyosin complex from Plasmodium falciparum Myosin A in the Rigor state
Components
  • Actin-1
  • Myosin-A
KeywordsMOTOR PROTEIN / Malaria / Plasmodium falciparum / Myosin A / invasion / Actin 1
Function / homology
Function and homology information


plastid inheritance / schizogony / pellicle / inner membrane pellicle complex / glideosome / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / entry into host cell by a symbiont-containing vacuole / myosin complex ...plastid inheritance / schizogony / pellicle / inner membrane pellicle complex / glideosome / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / entry into host cell by a symbiont-containing vacuole / myosin complex / microfilament motor activity / cytoskeletal motor activity / cytoskeleton organization / actin filament organization / actin filament / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / actin binding / ATP hydrolysis activity / ATP binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #20 / Alpha-Beta Plaits / Class XIV myosin, motor domain / Other non-globular / ATPase, substrate binding domain, subdomain 4 / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / Actin; Chain A, domain 4 ...Alpha-Beta Plaits - #20 / Alpha-Beta Plaits / Class XIV myosin, motor domain / Other non-globular / ATPase, substrate binding domain, subdomain 4 / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / Actin; Chain A, domain 4 / Kinesin motor domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Special / ATPase, nucleotide binding domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Jasplakinolide / ADENOSINE-5'-DIPHOSPHATE / Actin-1 / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsRobert-Paganin, J. / Xu, X.-P. / Swift, M.F. / Auguin, D. / Robblee, J.P. / Lu, H. / Fagnant, P.M. / Krementsova, E.B. / Trybus, K.M. / Houdusse, A. ...Robert-Paganin, J. / Xu, X.-P. / Swift, M.F. / Auguin, D. / Robblee, J.P. / Lu, H. / Fagnant, P.M. / Krementsova, E.B. / Trybus, K.M. / Houdusse, A. / Volkmann, N. / Hanein, D.
Funding support3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-AI132378
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10-OD012372
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10-OD026926
CitationJournal: Nat Commun / Year: 2021
Title: The actomyosin interface contains an evolutionary conserved core and an ancillary interface involved in specificity.
Authors: Julien Robert-Paganin / Xiao-Ping Xu / Mark F Swift / Daniel Auguin / James P Robblee / Hailong Lu / Patricia M Fagnant / Elena B Krementsova / Kathleen M Trybus / Anne Houdusse / Niels ...Authors: Julien Robert-Paganin / Xiao-Ping Xu / Mark F Swift / Daniel Auguin / James P Robblee / Hailong Lu / Patricia M Fagnant / Elena B Krementsova / Kathleen M Trybus / Anne Houdusse / Niels Volkmann / Dorit Hanein /
Abstract: Plasmodium falciparum, the causative agent of malaria, moves by an atypical process called gliding motility. Actomyosin interactions are central to gliding motility. However, the details of these ...Plasmodium falciparum, the causative agent of malaria, moves by an atypical process called gliding motility. Actomyosin interactions are central to gliding motility. However, the details of these interactions remained elusive until now. Here, we report an atomic structure of the divergent Plasmodium falciparum actomyosin system determined by electron cryomicroscopy at the end of the powerstroke (Rigor state). The structure provides insights into the detailed interactions that are required for the parasite to produce the force and motion required for infectivity. Remarkably, the footprint of the myosin motor on filamentous actin is conserved with respect to higher eukaryotes, despite important variability in the Plasmodium falciparum myosin and actin elements that make up the interface. Comparison with other actomyosin complexes reveals a conserved core interface common to all actomyosin complexes, with an ancillary interface involved in defining the spatial positioning of the motor on actin filaments.
History
DepositionOct 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-11818
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11818
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin-1
B: Actin-1
C: Actin-1
D: Actin-1
E: Actin-1
F: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,47319
Polymers302,0866
Non-polymers4,38713
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20450 Å2
ΔGint-161 kcal/mol
Surface area102610 Å2
MethodPISA

-
Components

#1: Protein
Actin-1 / Actin I


Mass: 41919.547 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFL2215w / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I4X0
#2: Protein Myosin-A / PfM-A


Mass: 92488.289 Da / Num. of mol.: 1 / Mutation: T417D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF13_0233 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDR3
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-9UE / Jasplakinolide


Mass: 709.670 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H45BrN4O6
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: actomyosin complex from Plasmodium falciparum / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -168.1 ° / Axial rise/subunit: 27.3 Å / Axial symmetry: C1
3D reconstructionResolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 464646 / Symmetry type: HELICAL

+
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