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- PDB-6i4l: Crystal Structure of Plasmodium falciparum actin I (G115A mutant)... -

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Basic information

Entry
Database: PDB / ID: 6i4l
TitleCrystal Structure of Plasmodium falciparum actin I (G115A mutant) in the Mg-K-ATP/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 / ADENOSINE-5'-TRIPHOSPHATE / 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: 1.83 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

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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)57,4299
Polymers56,2742
Non-polymers1,1557
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-59 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.450, 71.330, 110.310
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

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Actin-1 / Actin I


Mass: 42061.699 Da / Num. of mol.: 1 / Mutation: G115A
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 , 6 types, 387 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 48.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 23% PEG3350, 0.1M BIS-TRIS pH 5.9, 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: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.83→45.36 Å / Num. obs: 89639 / % possible obs: 95.93 % / Redundancy: 2 % / Biso Wilson estimate: 22.41 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1293 / Rpim(I) all: 0.1131 / Rrim(I) all: 0.1725 / Net I/σ(I): 4.96
Reflection shellResolution: 1.83→1.895 Å / Redundancy: 2 % / Rmerge(I) obs: 1.054 / Mean I/σ(I) obs: 0.65 / Num. unique obs: 8983 / CC1/2: 0.327 / Rpim(I) all: 0.9193 / Rrim(I) all: 1.404 / % possible all: 96.18

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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: 1.83→45.36 Å / SU ML: 0.3107 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 27.5482
RfactorNum. reflection% reflection
Rfree0.2428 4502 5.02 %
Rwork0.1996 --
obs0.2018 89595 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.57 Å2
Refinement stepCycle: LAST / Resolution: 1.83→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 67 380 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053987
X-RAY DIFFRACTIONf_angle_d0.73715421
X-RAY DIFFRACTIONf_chiral_restr0.0482587
X-RAY DIFFRACTIONf_plane_restr0.0046694
X-RAY DIFFRACTIONf_dihedral_angle_d10.24142345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.43761490.38452844X-RAY DIFFRACTION96.42
1.85-1.870.41321500.37082863X-RAY DIFFRACTION95.8
1.87-1.90.42621470.34982827X-RAY DIFFRACTION96.31
1.9-1.920.38531430.34322814X-RAY DIFFRACTION95.23
1.92-1.940.34591490.33112856X-RAY DIFFRACTION96.1
1.94-1.970.32081470.30682836X-RAY DIFFRACTION95.06
1.97-20.35791500.30612765X-RAY DIFFRACTION94.64
2-2.030.35741440.29272747X-RAY DIFFRACTION92.33
2.03-2.060.33941450.2922763X-RAY DIFFRACTION94.11
2.06-2.090.33771470.28242850X-RAY DIFFRACTION96.24
2.09-2.130.30611520.26812811X-RAY DIFFRACTION97.08
2.13-2.170.31631550.25472908X-RAY DIFFRACTION95.84
2.17-2.210.28841510.24382859X-RAY DIFFRACTION97.57
2.21-2.260.29721460.25232826X-RAY DIFFRACTION95.38
2.26-2.310.29171510.23472845X-RAY DIFFRACTION95.99
2.31-2.360.31591510.22652834X-RAY DIFFRACTION96.57
2.36-2.420.27481500.21742797X-RAY DIFFRACTION94.7
2.42-2.480.25111480.20612766X-RAY DIFFRACTION93.04
2.48-2.560.25411520.19712921X-RAY DIFFRACTION97.77
2.56-2.640.2641440.18552822X-RAY DIFFRACTION97.02
2.64-2.730.24481540.1832860X-RAY DIFFRACTION96.57
2.73-2.840.22941580.19232896X-RAY DIFFRACTION97.48
2.84-2.970.21911500.17762859X-RAY DIFFRACTION96.6
2.97-3.130.21651520.17642835X-RAY DIFFRACTION95.98
3.13-3.330.2291500.17562811X-RAY DIFFRACTION95.61
3.33-3.580.21291500.15682904X-RAY DIFFRACTION98.33
3.58-3.940.19291580.13912888X-RAY DIFFRACTION97.1
3.94-4.510.13441540.12382794X-RAY DIFFRACTION95.25
4.51-5.680.18911530.13342871X-RAY DIFFRACTION96.95
5.68-45.370.17441520.18052821X-RAY DIFFRACTION95.29

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