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- PDB-6i4k: Crystal Structure of Plasmodium falciparum actin I (G115A mutant)... -

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Basic information

Entry
Database: PDB / ID: 6i4k
TitleCrystal Structure of Plasmodium falciparum actin I (G115A mutant) in the Ca-ATP 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 / Neutrophil degranulation / actin cap / 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 / vesicle-mediated transport / phagocytic vesicle / 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 / actin cytoskeleton / lamellipodium / actin cytoskeleton organization / amyloid fibril formation / calcium ion binding / ATP hydrolysis activity / 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 / 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: 1.83 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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)57,44612
Polymers56,2742
Non-polymers1,17310
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-54 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.830, 71.380, 110.930
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-786-

HOH

21A-875-

HOH

31G-410-

HOH

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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 , 8 types, 527 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: 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
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.83→43.8 Å / Num. obs: 94327 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.02 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1356 / Rpim(I) all: 0.08056 / Rrim(I) all: 0.1582 / Net I/σ(I): 8.34
Reflection shellResolution: 1.83→1.895 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.1356 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 9298 / CC1/2: 0.373 / Rpim(I) all: 0.7318 / Rrim(I) all: 1.237 / % possible all: 98.52

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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→43.8 Å / SU ML: 0.1976 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 19.0791
RfactorNum. reflection% reflection
Rfree0.1967 4734 5.02 %
Rwork0.159 --
obs0.1609 94311 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.93 Å2
Refinement stepCycle: LAST / Resolution: 1.83→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 66 517 4387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664295
X-RAY DIFFRACTIONf_angle_d0.98455853
X-RAY DIFFRACTIONf_chiral_restr0.0526624
X-RAY DIFFRACTIONf_plane_restr0.0059767
X-RAY DIFFRACTIONf_dihedral_angle_d10.99742573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.32691500.33272910X-RAY DIFFRACTION97.42
1.85-1.870.30521560.30662978X-RAY DIFFRACTION98.96
1.87-1.90.31481580.28992945X-RAY DIFFRACTION99.17
1.9-1.920.33421600.26943008X-RAY DIFFRACTION99.75
1.92-1.940.27341550.2482989X-RAY DIFFRACTION99.87
1.94-1.970.24791550.24452943X-RAY DIFFRACTION100
1.97-20.28691620.23713027X-RAY DIFFRACTION99.97
2-2.030.241580.21982984X-RAY DIFFRACTION100
2.03-2.060.2581610.21553030X-RAY DIFFRACTION99.97
2.06-2.090.24441570.20552971X-RAY DIFFRACTION100
2.09-2.130.26191590.18582989X-RAY DIFFRACTION100
2.13-2.170.19541590.18782980X-RAY DIFFRACTION100
2.17-2.210.23371550.17922972X-RAY DIFFRACTION99.84
2.21-2.260.20721610.1693023X-RAY DIFFRACTION100
2.26-2.310.17041560.16153000X-RAY DIFFRACTION99.94
2.31-2.360.23271590.1572957X-RAY DIFFRACTION99.97
2.36-2.420.18441540.15142974X-RAY DIFFRACTION99.94
2.42-2.480.21161590.14843040X-RAY DIFFRACTION99.97
2.48-2.560.16791550.14452970X-RAY DIFFRACTION99.97
2.56-2.640.20321580.14332984X-RAY DIFFRACTION99.97
2.64-2.730.16281530.14022997X-RAY DIFFRACTION99.97
2.73-2.840.18371610.142982X-RAY DIFFRACTION100
2.84-2.970.1981600.14383003X-RAY DIFFRACTION99.94
2.97-3.130.17831650.14512995X-RAY DIFFRACTION100
3.13-3.330.16661600.13992964X-RAY DIFFRACTION100
3.33-3.580.18261590.12983006X-RAY DIFFRACTION99.97
3.58-3.940.16661630.12122973X-RAY DIFFRACTION100
3.94-4.510.1551540.10393004X-RAY DIFFRACTION100
4.51-5.680.14971610.11592983X-RAY DIFFRACTION99.9
5.68-45.530.17771510.16852996X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90499189037-1.334383023890.6812761485923.055897537432.235995488232.823861369450.240418818479-0.410818480450.7310255751570.364089483272-0.09630190507690.158750050318-0.79202971176-0.2076280856740.1497798806780.4966929803330.01288491397110.109845800890.27713910792-0.05291853435770.3573691394868.3814074703523.3430651939148.281012138
20.753842862501-0.272812069865-0.06849279782681.7942473669-0.2581516322640.584378805097-0.03160328928550.06719657122690.0981645385856-0.02607874953420.04157907780890.0440315895861-0.08421170556610.0141002103738-0.01390070598870.163198839569-0.0143631136754-0.02465907225470.1852617792720.01042172756780.15529254978616.176473659815.6952907928122.571881827
31.229828793190.314635520838-0.2807400891281.206548027130.06992881476441.846281133460.0184516226411-0.165346798383-0.09097655326470.127079339057-0.0203138361445-0.05064264480960.07616482483970.14245504871-0.02702631274020.1544120905430.00177604878386-0.00881372215480.2098732005930.01618024604640.14595326124911.81730521311.01500992535146.666286545
42.27675740169-0.253960440970.3635630659632.132776382250.01348979875982.318177227740.0551198884614-0.00828663412846-0.2120588408910.00413011560147-0.0262804152087-0.1546554313530.1416764006380.04641659155440.02029084143440.155251529383-0.0125144588932-0.005231991009130.1343328478750.01452418859440.17264853893410.7533723292-18.9615095272124.465663473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 5 through 33 or resid 75 through 137 or resid 339 through 375 )
4X-RAY DIFFRACTION4chain 'G' and (resid 27 through 150 )

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