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- PDB-6i4e: Crystal Structure of Plasmodium falciparum actin I in the Mg-ADP state -

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Basic information

Entry
Database: PDB / ID: 6i4e
TitleCrystal Structure of Plasmodium falciparum actin I in the Mg-ADP state
Components
  • Actin-1
  • Gelsolin
KeywordsCONTRACTILE PROTEIN / hydrolase / filamentous / glideosome / cytoskeleton
Function / homology
Function and homology information


plastid inheritance / schizogony / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / Caspase-mediated cleavage of cytoskeletal proteins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption ...plastid inheritance / schizogony / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / Caspase-mediated cleavage of cytoskeletal proteins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / Neutrophil degranulation / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / entry into host cell by a symbiont-containing vacuole / actin filament capping / actin filament depolymerization / cardiac muscle cell contraction / relaxation of cardiac muscle / podosome / phagocytosis, engulfment / hepatocyte apoptotic process / sarcoplasm / cilium assembly / phagocytic vesicle / vesicle-mediated transport / response to muscle stretch / actin filament polymerization / Neutrophil degranulation / cytoskeleton organization / actin filament / protein destabilization / cellular response to type II interferon / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / lamellipodium / actin cytoskeleton / actin cytoskeleton organization / amyloid fibril formation / calcium ion binding / ATP hydrolysis activity / extracellular space / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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'-DIPHOSPHATE / BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Gelsolin / Actin-1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsKumpula, E.-P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I.
Funding support Finland, Norway, 3items
OrganizationGrant numberCountry
Academy of Finland Finland
Sigrid Juselius Foundation Finland
Research Council of Norway Norway
CitationJournal: Plos Biol. / Year: 2019
Title: Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation.
Authors: Kumpula, E.P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I.
History
DepositionNov 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin-1
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,41913
Polymers56,2602
Non-polymers1,16011
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-57 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.520, 71.270, 109.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-819-

HOH

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Actin-1 / Actin I


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)
Gene: PFL2215w / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I4X0
#2: Protein Gelsolin / Actin-depolymerizing factor / ADF / Brevin


Mass: 14211.929 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsn, Gsb / Production host: Escherichia coli (E. coli) / References: UniProt: P13020

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Non-polymers , 8 types, 456 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#8: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 23% PEG3350, 0.1M BIS-TRIS pH 6.2, 0.2M K-SCN; 20% PEG400 used for cryoprotection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.22→49.39 Å / Num. obs: 159860 / % possible obs: 99.79 % / Redundancy: 5.4 % / Biso Wilson estimate: 14.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0471 / Rpim(I) all: 0.02243 / Rrim(I) all: 0.05232 / Net I/σ(I): 16.29
Reflection shellResolution: 1.22→1.264 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.129 / Num. unique obs: 15809 / CC1/2: 0.513 / Rpim(I) all: 0.5293 / Rrim(I) all: 1.25 / % possible all: 99.75

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBU

4cbu


Resolution: 1.22→49.39 Å / SU ML: 0.1106 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.1772
RfactorNum. reflection% reflection
Rfree0.1567 7993 5 %
Rwork0.1357 --
obs0.1367 159854 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.71 Å2
Refinement stepCycle: LAST / Resolution: 1.22→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3719 0 66 445 4230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01094641
X-RAY DIFFRACTIONf_angle_d1.1676367
X-RAY DIFFRACTIONf_chiral_restr0.0895665
X-RAY DIFFRACTIONf_plane_restr0.0087859
X-RAY DIFFRACTIONf_dihedral_angle_d14.46941792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.230.27662620.2634972X-RAY DIFFRACTION99.49
1.23-1.250.29132650.25155029X-RAY DIFFRACTION99.81
1.25-1.260.2422630.23655005X-RAY DIFFRACTION99.68
1.26-1.280.2282610.2224949X-RAY DIFFRACTION99.66
1.28-1.30.22552680.21095089X-RAY DIFFRACTION99.68
1.3-1.310.25682610.2094971X-RAY DIFFRACTION99.83
1.31-1.330.22922650.19445029X-RAY DIFFRACTION99.81
1.33-1.350.19822650.18755028X-RAY DIFFRACTION99.91
1.35-1.370.2182650.17515035X-RAY DIFFRACTION99.87
1.37-1.40.19392650.17865047X-RAY DIFFRACTION99.96
1.4-1.420.1932620.15954978X-RAY DIFFRACTION99.94
1.42-1.450.19962640.15145035X-RAY DIFFRACTION99.92
1.45-1.470.17382660.13525042X-RAY DIFFRACTION99.96
1.47-1.50.15812660.1185057X-RAY DIFFRACTION99.98
1.5-1.540.14692640.1125017X-RAY DIFFRACTION99.94
1.54-1.570.14082670.10725069X-RAY DIFFRACTION99.96
1.57-1.610.142640.10265024X-RAY DIFFRACTION99.89
1.61-1.660.14762680.10645071X-RAY DIFFRACTION99.91
1.66-1.70.13682670.10725072X-RAY DIFFRACTION99.98
1.7-1.760.1512660.1125060X-RAY DIFFRACTION100
1.76-1.820.13692670.10615069X-RAY DIFFRACTION99.98
1.82-1.90.13692670.11355082X-RAY DIFFRACTION99.89
1.9-1.980.1482670.11565057X-RAY DIFFRACTION99.76
1.98-2.090.14672680.11485088X-RAY DIFFRACTION99.93
2.09-2.220.14082680.1125090X-RAY DIFFRACTION99.94
2.22-2.390.14092680.11825115X-RAY DIFFRACTION99.91
2.39-2.630.14822700.12725125X-RAY DIFFRACTION99.74
2.63-3.010.16042700.14195138X-RAY DIFFRACTION99.39
3.01-3.790.14452720.13835155X-RAY DIFFRACTION98.82
3.79-49.440.14812820.14565363X-RAY DIFFRACTION99.14

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