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- PDB-4cbu: Crystal structure of Plasmodium falciparum actin I -

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Basic information

Entry
Database: PDB / ID: 4cbu
TitleCrystal structure of Plasmodium falciparum actin I
Components
  • ACTIN-1
  • GELSOLIN
KeywordsMOTOR PROTEIN / MALARIA / MOTILITY / PARASITE
Function / homology
Function and homology information


glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / actin polymerization-dependent cell-to-cell migration in host / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption ...glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / actin polymerization-dependent cell-to-cell migration in host / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / sarcoplasm / positive regulation of p38MAPK cascade / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / positive regulation of cardiac muscle hypertrophy / hepatocyte apoptotic process / cilium assembly / phagocytic vesicle / vesicle-mediated transport / ruffle / cellular response to cadmium ion / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / Neutrophil degranulation / central nervous system development / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / structural constituent of cytoskeleton / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / myelin sheath / actin binding / actin cytoskeleton organization / amyloid fibril formation / hydrolase activity / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / protein-containing complex / extracellular space / extracellular region / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain ...Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / 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 / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin / Actin-1
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVahokoski, J. / Bhargav, S.P. / Desfosses, A. / Andreadaki, M. / Kumpula, E.P. / Ignatev, A. / Munico Martinez, S. / Lepper, S. / Frischknecht, F. / Siden-Kiamos, I. ...Vahokoski, J. / Bhargav, S.P. / Desfosses, A. / Andreadaki, M. / Kumpula, E.P. / Ignatev, A. / Munico Martinez, S. / Lepper, S. / Frischknecht, F. / Siden-Kiamos, I. / Sachse, C. / Kursula, I.
CitationJournal: PLoS Pathog / Year: 2014
Title: Structural differences explain diverse functions of Plasmodium actins.
Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht ...Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht / Inga Sidén-Kiamos / Carsten Sachse / Inari Kursula /
Abstract: Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also ...Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties.
History
DepositionOct 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIN-1
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8876
Polymers56,2602
Non-polymers6274
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-52.4 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.980, 110.300, 71.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2390-

HOH

21A-2680-

HOH

31A-2721-

HOH

41A-2760-

HOH

51G-2650-

HOH

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Components

#1: Protein ACTIN-1 / / ACTIN I / PFACT1 / ACTIN


Mass: 42047.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: P86287
#2: Protein GELSOLIN / / ACTIN-DEPOLYMERIZING FACTOR / ADF / BREVIN


Mass: 14211.929 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P13020
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6.5
Details: 22%(W/V) PEG 3350, 0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS-TRIS PROPANE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→55 Å / Num. obs: 134201 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 10.69 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.65 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→55.15 Å / SU ML: 0.11 / σ(F): 1.99 / Phase error: 13.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1534 4040 3 %
Rwork0.1205 --
obs0.1215 134194 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.96 Å2
Refinement stepCycle: LAST / Resolution: 1.3→55.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 34 774 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124589
X-RAY DIFFRACTIONf_angle_d1.4816301
X-RAY DIFFRACTIONf_dihedral_angle_d14.5711767
X-RAY DIFFRACTIONf_chiral_restr0.098660
X-RAY DIFFRACTIONf_plane_restr0.009850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31530.26241500.25024318X-RAY DIFFRACTION98
1.3153-1.33130.25151250.22444424X-RAY DIFFRACTION100
1.3313-1.34820.27011280.21044492X-RAY DIFFRACTION100
1.3482-1.36590.23131350.19164398X-RAY DIFFRACTION100
1.3659-1.38470.20971450.18314465X-RAY DIFFRACTION100
1.3847-1.40440.20491410.16214450X-RAY DIFFRACTION100
1.4044-1.42540.21541230.15154458X-RAY DIFFRACTION100
1.4254-1.44770.19621440.14414451X-RAY DIFFRACTION100
1.4477-1.47140.15941310.13144460X-RAY DIFFRACTION100
1.4714-1.49680.16991500.12144458X-RAY DIFFRACTION100
1.4968-1.5240.16741300.11464459X-RAY DIFFRACTION100
1.524-1.55330.14991570.10834437X-RAY DIFFRACTION100
1.5533-1.5850.15281340.10114466X-RAY DIFFRACTION100
1.585-1.61950.13651360.09924464X-RAY DIFFRACTION100
1.6195-1.65720.13971230.09494490X-RAY DIFFRACTION100
1.6572-1.69860.13571400.08874448X-RAY DIFFRACTION100
1.6986-1.74450.14471380.08914510X-RAY DIFFRACTION100
1.7445-1.79590.13031380.09064431X-RAY DIFFRACTION100
1.7959-1.85390.11451300.08834518X-RAY DIFFRACTION100
1.8539-1.92010.12441280.09024500X-RAY DIFFRACTION100
1.9201-1.9970.12971400.08924485X-RAY DIFFRACTION100
1.997-2.08790.12821190.08974537X-RAY DIFFRACTION100
2.0879-2.1980.11551570.09744484X-RAY DIFFRACTION100
2.198-2.33570.12471490.09854502X-RAY DIFFRACTION100
2.3357-2.5160.14781330.10424547X-RAY DIFFRACTION100
2.516-2.76920.13611470.11714547X-RAY DIFFRACTION100
2.7692-3.16990.15141510.12784571X-RAY DIFFRACTION100
3.1699-3.99360.1481560.12514598X-RAY DIFFRACTION100
3.9936-55.19970.17951620.15064786X-RAY DIFFRACTION100

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