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- PDB-6tu7: Structure of PfMyoA decorated Plasmodium Act1 filament -

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Basic information

Entry
Database: PDB / ID: 6tu7
TitleStructure of PfMyoA decorated Plasmodium Act1 filament
Components
  • Actin-1
  • Myosin-A
KeywordsMOTOR PROTEIN / malaria / Plasmodium falciparum / myosin / unconventional / filament
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
Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / 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. / 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 / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Jasplakinolide / ADENOSINE-5'-DIPHOSPHATE / Actin-1 / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVahokoski, J. / Calder, L.J. / Lopez, A.J. / Rosenthal, P.B. / Kursula, I.
Funding support Norway, United Kingdom, 2items
OrganizationGrant numberCountry
Norwegian Research Council Norway
The Francis Crick Institute United Kingdom
CitationJournal: PLoS Pathog / Year: 2022
Title: High-resolution structures of malaria parasite actomyosin and actin filaments.
Authors: Juha Vahokoski / Lesley J Calder / Andrea J Lopez / Justin E Molloy / Inari Kursula / Peter B Rosenthal /
Abstract: Malaria is responsible for half a million deaths annually and poses a huge economic burden on the developing world. The mosquito-borne parasites (Plasmodium spp.) that cause the disease depend upon ...Malaria is responsible for half a million deaths annually and poses a huge economic burden on the developing world. The mosquito-borne parasites (Plasmodium spp.) that cause the disease depend upon an unconventional actomyosin motor for both gliding motility and host cell invasion. The motor system, often referred to as the glideosome complex, remains to be understood in molecular terms and is an attractive target for new drugs that might block the infection pathway. Here, we present the high-resolution structure of the actomyosin motor complex from Plasmodium falciparum. The complex includes the malaria parasite actin filament (PfAct1) complexed with the class XIV myosin motor (PfMyoA) and its two associated light-chains. The high-resolution core structure reveals the PfAct1:PfMyoA interface in atomic detail, while at lower-resolution, we visualize the PfMyoA light-chain binding region, including the essential light chain (PfELC) and the myosin tail interacting protein (PfMTIP). Finally, we report a bare PfAct1 filament structure at improved resolution.
History
DepositionJan 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
AP1: Myosin-A
BP1: Actin-1
CP1: Actin-1
DP1: Actin-1
EP1: Actin-1
GP1: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,18618
Polymers353,5426
Non-polymers4,64512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17430 Å2
ΔGint-143 kcal/mol
Surface area126220 Å2
MethodPISA

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Components

#1: Protein Myosin-A / PfM-A


Mass: 92675.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF13_0233 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDR3
#2: Protein
Actin-1 / Actin I


Mass: 42047.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFL2215w / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I4X0
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-9UE / Jasplakinolide


Mass: 709.670 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H45BrN4O6
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PfMyoA decorated PfAct1 filament / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 49.2 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.16_3549refinement
PHENIX1.16_3549refinement
EM software
IDNameVersionCategory
7UCSF Chimera1.13model fitting
12RELION3.0 beta3D reconstruction
13PHENIX1.16-3549model refinement
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -166.498 ° / Axial rise/subunit: 28.3417 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239021 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
15OGW

5ogw

A5OGW1
26I7D

6i7d

D6I7D2
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.35 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00624546
ELECTRON MICROSCOPYf_angle_d0.554833206
ELECTRON MICROSCOPYf_chiral_restr0.04713712
ELECTRON MICROSCOPYf_plane_restr0.0044252
ELECTRON MICROSCOPYf_dihedral_angle_d14.107214770

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