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- PDB-6tu4: Structure of Plasmodium Actin1 filament -

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Basic information

Entry
Database: PDB / ID: 6tu4
TitleStructure of Plasmodium Actin1 filament
ComponentsActin-1
KeywordsMOTOR PROTEIN / malaria / Plasmodium falciparum / myosin / unconventional / filament
Function / homology
Function and homology information


plastid inheritance / schizogony / 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 / cytoskeleton organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...plastid inheritance / schizogony / 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 / cytoskeleton organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / actin cytoskeleton / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Jasplakinolide / ADENOSINE-5'-DIPHOSPHATE / Actin-1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 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 2, 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

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)216,04420
Polymers210,2385
Non-polymers5,80615
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, https://doi.org/10.1371/journal.pbio.3000315
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15500 Å2
ΔGint-139 kcal/mol
Surface area78120 Å2
MethodPISA

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Components

#1: Protein
Actin-1 / / Actin I


Mass: 42047.676 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: codon optimised gene / Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFL2215w / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I4X0
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Mg
#3: Chemical
ChemComp-9UE / Jasplakinolide


Mass: 709.670 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H45BrN4O6
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: PfAct1 filament / Type: COMPLEX / Entity ID: #1 / 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 FIELDBright-field microscopy
Image recordingElectron dose: 51.52 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
7UCSF Chimera1.13model fitting
9PHENIX1.17-3644model refinement
13RELION3.0.73D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -167.652 ° / Axial rise/subunit: 28.3692 Å / Axial symmetry: C1
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305480 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5OGW

5ogw


Pdb chain-ID: A
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 37.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003116010
ELECTRON MICROSCOPYf_angle_d0.608821898
ELECTRON MICROSCOPYf_chiral_restr0.0492448
ELECTRON MICROSCOPYf_plane_restr0.00482805
ELECTRON MICROSCOPYf_dihedral_angle_d19.77036132

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