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- PDB-8ccn: Filamentous actin II from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 8ccn
TitleFilamentous actin II from Plasmodium falciparum
ComponentsActin-2
KeywordsCELL INVASION / Filament-forming male-gametogenesis Zygote Hydrolase ATP-binding malaria methylation
Function / homology
Function and homology information


Platelet degranulation / 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 / microfilament motor activity / cytoskeleton organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / hydrolase activity ...Platelet degranulation / 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 / microfilament motor activity / cytoskeleton organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / hydrolase activity / ATP binding / 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
ADENOSINE-5'-DIPHOSPHATE / Actin-2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKursula, I. / Lopez, A.J.
Funding support Finland, Norway, United Kingdom, 5items
OrganizationGrant numberCountry
Academy of Finland Finland
Norwegian Research Council Norway
Sigrid Juselius Foundation Finland
Cancer Research UK United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: PLoS Pathog / Year: 2023
Title: Structure and function of Plasmodium actin II in the parasite mosquito stages.
Authors: Andrea J Lopez / Maria Andreadaki / Juha Vahokoski / Elena Deligianni / Lesley J Calder / Serena Camerini / Anika Freitag / Ulrich Bergmann / Peter B Rosenthal / Inga Sidén-Kiamos / Inari Kursula /
Abstract: Actins are filament-forming, highly-conserved proteins in eukaryotes. They are involved in essential processes in the cytoplasm and also have nuclear functions. Malaria parasites (Plasmodium spp.) ...Actins are filament-forming, highly-conserved proteins in eukaryotes. They are involved in essential processes in the cytoplasm and also have nuclear functions. Malaria parasites (Plasmodium spp.) have two actin isoforms that differ from each other and from canonical actins in structure and filament-forming properties. Actin I has an essential role in motility and is fairly well characterized. The structure and function of actin II are not as well understood, but mutational analyses have revealed two essential functions in male gametogenesis and in the oocyst. Here, we present expression analysis, high-resolution filament structures, and biochemical characterization of Plasmodium actin II. We confirm expression in male gametocytes and zygotes and show that actin II is associated with the nucleus in both stages in filament-like structures. Unlike actin I, actin II readily forms long filaments in vitro, and near-atomic structures in the presence or absence of jasplakinolide reveal very similar structures. Small but significant differences compared to other actins in the openness and twist, the active site, the D-loop, and the plug region contribute to filament stability. The function of actin II was investigated through mutational analysis, suggesting that long and stable filaments are necessary for male gametogenesis, while a second function in the oocyst stage also requires fine-tuned regulation by methylation of histidine 73. Actin II polymerizes via the classical nucleation-elongation mechanism and has a critical concentration of ~0.1 μM at the steady-state, like actin I and canonical actins. Similarly to actin I, dimers are a stable form of actin II at equilibrium.
History
DepositionJan 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Aug 23, 2023Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code ..._entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-2
B: Actin-2
C: Actin-2
D: Actin-2
E: Actin-2
F: Actin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,49018
Polymers256,7816
Non-polymers2,70912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "D" and (resid 5 through 94 or resid 96...
d_2ens_1(chain "B" and (resid 5 through 94 or resid 96...
d_3ens_1(chain "C" and (resid 5 through 94 or resid 96...
d_4ens_1(chain "A" and (resid 5 through 94 or resid 96...
d_5ens_1(chain "E" and (resid 5 through 94 or resid 96...
d_6ens_1(chain "F" and (resid 5 through 94 or resid 96...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALALEUB1 - 90
d_12ens_1VALGLUB92 - 201
d_13ens_1GLULYSB203 - 224
d_14ens_1SERMETB226 - 322
d_15ens_1ILEHISB324 - 368
d_16ens_1LYSPHEB370 - 372
d_17ens_1ADPADPK
d_21ens_1ALALEUD1 - 90
d_22ens_1VALGLUD92 - 201
d_23ens_1GLULYSD203 - 224
d_24ens_1SERMETD226 - 322
d_25ens_1ILEHISD324 - 368
d_26ens_1LYSPHED370 - 372
d_27ens_1ADPADPE
d_31ens_1ALALEUG1 - 90
d_32ens_1VALGLUG92 - 201
d_33ens_1GLULYSG203 - 224
d_34ens_1SERMETG226 - 322
d_35ens_1ILEHISG324 - 368
d_36ens_1LYSPHEG370 - 372
d_37ens_1ADPADPH
d_41ens_1ALALEUA1 - 90
d_42ens_1VALGLUA92 - 201
d_43ens_1GLULYSA203 - 224
d_44ens_1SERMETA226 - 322
d_45ens_1ILEHISA324 - 368
d_46ens_1LYSPHEA370 - 372
d_47ens_1ADPADPB
d_51ens_1ALALEUM1 - 90
d_52ens_1VALGLUM92 - 201
d_53ens_1GLULYSM203 - 224
d_54ens_1SERMETM226 - 322
d_55ens_1ILEHISM324 - 368
d_56ens_1LYSPHEM370 - 372
d_57ens_1ADPADPN
d_61ens_1ALALEUP1 - 90
d_62ens_1VALGLUP92 - 201
d_63ens_1GLULYSP203 - 224
d_64ens_1SERMETP226 - 322
d_65ens_1ILEHISP324 - 368
d_66ens_1LYSPHEP370 - 372
d_67ens_1ADPADPQ

NCS oper:
IDCodeMatrixVector
1given(0.897587305352, 0.440836291179, -0.000627415703053), (-0.440836309876, 0.897587508003, 0.000115638948349), (0.000614138342491, 0.00017279157125, 0.999999796489)-60.3667847108, 97.0851012764, -56.8217746871
2given(-0.974113281191, -0.226060421982, 3.19623241049E-5), (0.226060422573, -0.974113281443, 1.62205560151E-5), (2.74680986788E-5, 2.30260755362E-5, 0.999999999358)393.301673138, 312.48741319, -28.3456628709
3given(-0.774423801614, -0.632666958364, 0.000543404361041), (0.632666989994, -0.77442395493, -0.000133422768307), (0.000505237531405, 0.000240468233996, 0.999999843455)430.184888464, 204.129875649, -85.1552693006
4given(-0.973922593499, 0.226880543519, -2.90674870155E-5), (-0.226880545335, -0.97392258789, 0.000104620711845), (-4.57307821097E-6, 0.000108487322319, 0.999999994105)312.309598513, 393.402712455, 28.3251072324
5given(0.898116955605, -0.439755943931, 0.000802391785824), (0.439755172487, 0.898117161253, 0.000976183433163), (-0.0011499243, -0.000523870954927, 0.999999201616)96.6389632404, -60.5673735842, 56.9842556691

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Components

#1: Protein
Actin-2 / Actin II


Mass: 42796.879 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ACT2, ACTII, PF14_0124, PF3D7_1412500 / Plasmid: pFastBacTHT A / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8ILW9, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: Actin II filaments / Type: COMPLEX / Details: Actin in the ADP-Mg state / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 / Plasmid: pFastBacTHT A
Buffer solutionpH: 7.5
Details: 10 mM HEPES pH 7.5, 0.2 mM CaCl2, 0.5 mM ATP, 0.5 mM TCEP, 4 mM MgCl2, 50 mM KCl, 10 mM EGTA
SpecimenConc.: 0.21 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 47.2 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1058

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
1RELION3.1betaparticle selection
4CTFFIND4.1.10CTF correction
7UCSF Chimera1.14model fitting
9PHENIXmodel refinement
13RELION3.1beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.9 ° / Axial rise/subunit: 28.34 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 49102
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47197 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 49.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001518522
ELECTRON MICROSCOPYf_angle_d0.468225134
ELECTRON MICROSCOPYf_chiral_restr0.04212772
ELECTRON MICROSCOPYf_plane_restr0.0033210
ELECTRON MICROSCOPYf_dihedral_angle_d7.09387116
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BELECTRON MICROSCOPYNCS constraints0.000709136676221
ens_1d_3BELECTRON MICROSCOPYNCS constraints0.000715163735657
ens_1d_4BELECTRON MICROSCOPYNCS constraints0.000703819402875
ens_1d_5BELECTRON MICROSCOPYNCS constraints0.000712952335147
ens_1d_6BELECTRON MICROSCOPYNCS constraints0.000711439259774

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