[English] 日本語
Yorodumi
- EMDB-11818: Cryo-EM structure of the divergent actomyosin complex from Plasmo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11818
TitleCryo-EM structure of the divergent actomyosin complex from Plasmodium falciparum Myosin A in the Rigor state
Map data
Sample
  • Complex: actomyosin complex from Plasmodium falciparumMyofilament
    • Protein or peptide: Actin-1
    • Protein or peptide: Myosin-A
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: Jasplakinolide
Function / homology
Function and homology information


plastid inheritance / schizogony / pellicle / glideosome / inner membrane pellicle complex / Platelet degranulation / 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 ...plastid inheritance / schizogony / pellicle / glideosome / inner membrane pellicle complex / Platelet degranulation / 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 / vesicle transport along actin filament / myosin complex / microfilament motor activity / cytoskeletal motor activity / cytoskeleton organization / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / actin filament binding / actin cytoskeleton / actin binding / vesicle / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site ...Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (isolate 3D7) (eukaryote)
Methodhelical reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsRobert-Paganin J / Xu X-P / Swift MF / Auguin D / Robblee JP / Lu H / Fagnant PM / Krementsova EB / Trybus KM / Houdusse A ...Robert-Paganin J / Xu X-P / Swift MF / Auguin D / Robblee JP / Lu H / Fagnant PM / Krementsova EB / Trybus KM / Houdusse A / Volkmann N / Hanein D
Funding support3 items
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, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7aln
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7aln
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11818.png

Downloads & links

-
Map

FileDownload / File: emd_11818.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.035 Å
Density
Contour LevelBy AUTHOR: 4.0 / Movie #1: 6
Minimum - Maximum-4.928446 - 35.041412
Average (Standard dev.)0.09540938 (±1.3107578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin666
Dimensions336336336
Spacing336336336
CellA=B=C: 347.75998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0351.0351.035
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z347.760347.760347.760
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS666
NC/NR/NS336336336
D min/max/mean-4.92835.0410.095

-
Supplemental data

-
Sample components

-
Entire : actomyosin complex from Plasmodium falciparum

EntireName: actomyosin complex from Plasmodium falciparumMyofilament
Components
  • Complex: actomyosin complex from Plasmodium falciparumMyofilament
    • Protein or peptide: Actin-1
    • Protein or peptide: Myosin-A
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: Jasplakinolide

-
Supramolecule #1: actomyosin complex from Plasmodium falciparum

SupramoleculeName: actomyosin complex from Plasmodium falciparum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

-
Macromolecule #1: Actin-1

MacromoleculeName: Actin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 41.919547 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGEEDVQALV VDNGSGNVKA GVAGDDAPRS VFPSIVGRPK NPGIMVGMEE KDAFVGDEAQ TKRGILTLKY PIEHGIVTNW DDMEKIWHH TFYNELRAAP EEHPVLLTEA PLNPKGNRER MTQIMFESFN VPAMYVAIQA VLSLYSSGRT TGIVLDSGDG V SHTVPIYE ...String:
MGEEDVQALV VDNGSGNVKA GVAGDDAPRS VFPSIVGRPK NPGIMVGMEE KDAFVGDEAQ TKRGILTLKY PIEHGIVTNW DDMEKIWHH TFYNELRAAP EEHPVLLTEA PLNPKGNRER MTQIMFESFN VPAMYVAIQA VLSLYSSGRT TGIVLDSGDG V SHTVPIYE GYALPHAIMR LDLAGRDLTE YLMKILHERG YGFSTSAEKE IVRDIKEKLC YIALNFDEEM KTSEQSSDIE KS YELPDGN IITVGNERFR CPEALFQPSF LGKEAAGIHT TTFNSIKKCD VDIRKDLYGN IVLSGGTTMY EGIGERLTRD ITT LAPSTM KIKVVAPPER KYSVWIGGSI LSSLSTFQQM WITKEEYDES GPSIVHRKCF

-
Macromolecule #2: Myosin-A

MacromoleculeName: Myosin-A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 92.488289 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAVTNEEIKT ASKIVRRV(SEP)N VEAFDKSGSV FKGYQIWTDI SPTIENDPNI MFVKCVVQQG SKKEKLTVVQ IDPPGT GTP YDIDPTHAWN CNSQVDPMSF GDIGLLNHTN IPCVLDFLKH RYLKNQIYTT AVPLIVAINP YKDLGNTTNE WIRRYRD TA DHTKLPPHVF ...String:
MAVTNEEIKT ASKIVRRV(SEP)N VEAFDKSGSV FKGYQIWTDI SPTIENDPNI MFVKCVVQQG SKKEKLTVVQ IDPPGT GTP YDIDPTHAWN CNSQVDPMSF GDIGLLNHTN IPCVLDFLKH RYLKNQIYTT AVPLIVAINP YKDLGNTTNE WIRRYRD TA DHTKLPPHVF TCAREALSNL HGVNKSQTII VSGESGAGKT EATKQIMRYF ASSKSGNMDL RIQTAIMAAN PVLEAFGN A KTIRNNNSSR FGRFMQLVIS HEGGIRYGSV VAFLLEKSRI ITQDDNERSY HIFYQFLKGA NSTMKSKFGL KGVTEYKLL NPNSTEVSGV DDVKDFEEVI ESLKNMELSE SDIEVIFSIV AGILTLGNVR LIEKQEAGLS DAAAIMDEDM GVFNKACELM YLDPELIKR EILIKVTVAG GDKIEGRWNK NDAEVLKSSL CKAMYEKLFL WIIRHLNSRI EPEGGFKTFM GMLDIFGFEV F KNNSLEQL FINITNEMLQ KNFVDIVFER ESKLYKDEGI STAELKYTSN KEVINVLCEK GKSVLSYLED QCLAPGGTDE KF VSSCATN LKENNKFTPA KVASNKNFII QHTIGPIQYC AESFLLKNKD VLRGDLVEVI KDSPNPIVQQ LFEGQVIEKG KIA KGSLIG SQFLNQLTSL MNLINSTEPH FIRCIKPNEN KKPLEWCEPK ILIQLHALSI LEALVLRQLG YSYRRTFEEF LYQY KFVDI AAAEDSSVEN QNKCVNILKL SGLSESMYKI GKSMVFLKQE GAKILTKIQR EKLVEWENCV SVIEAAILKH KYKQK VNKN IPSLLRVQAH IRKKMVAQ

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: Jasplakinolide

MacromoleculeName: Jasplakinolide / type: ligand / ID: 5 / Number of copies: 3 / Formula: 9UE
Molecular weightTheoretical: 709.67 Da
Chemical component information

ChemComp-9UE:
Jasplakinolide

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: in-house rabbit actin map filtered to 40A
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.3 Å
Applied symmetry - Helical parameters - Δ&Phi: -168.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 464646

+
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