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- PDB-6i4i: Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) ... -

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Basic information

Entry
Database: PDB / ID: 6i4i
TitleCrystal Structure of Plasmodium falciparum actin I (F54Y mutant) in the Mg-K-ADP-AlFn 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 / 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 / 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 / ALUMINUM FLUORIDE / : / 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: 1.9 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_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)57,02810
Polymers56,2762
Non-polymers7528
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-53 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.610, 71.330, 109.250
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-664-

HOH

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Actin-1 / Actin I


Mass: 42063.676 Da / Num. of mol.: 1 / Mutation: F54Y
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 , 7 types, 279 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-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#8: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
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: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.9→45.05 Å / Num. obs: 81327 / % possible obs: 99.46 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09613 / Rpim(I) all: 0.06149 / Rrim(I) all: 0.1146 / Net I/σ(I): 9.06
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.7099 / Num. unique obs: 8100 / CC1/2: 0.591 / Rpim(I) all: 0.4566 / Rrim(I) all: 0.8476 / % possible all: 99.11

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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: 1.9→45.05 Å / SU ML: 0.3021 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 24.9267
RfactorNum. reflection% reflection
Rfree0.217 4059 5 %
Rwork0.1787 --
obs0.1806 81217 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 39 271 4049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774026
X-RAY DIFFRACTIONf_angle_d0.89275473
X-RAY DIFFRACTIONf_chiral_restr0.0523590
X-RAY DIFFRACTIONf_plane_restr0.0058714
X-RAY DIFFRACTIONf_dihedral_angle_d10.70182406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.47151430.44652624X-RAY DIFFRACTION98.79
1.92-1.950.36361410.36082659X-RAY DIFFRACTION99.47
1.95-1.970.3541360.32512664X-RAY DIFFRACTION99.01
1.97-20.2961430.29672654X-RAY DIFFRACTION99.4
2-2.020.32971400.31482678X-RAY DIFFRACTION99.4
2.02-2.050.33671330.33252607X-RAY DIFFRACTION99.13
2.05-2.080.34651410.33672676X-RAY DIFFRACTION98.39
2.08-2.120.30011400.30342660X-RAY DIFFRACTION99.19
2.12-2.150.32491410.25782640X-RAY DIFFRACTION99.61
2.15-2.190.29241390.22722660X-RAY DIFFRACTION99.71
2.19-2.230.30011340.23552657X-RAY DIFFRACTION99.57
2.23-2.270.30811400.24982665X-RAY DIFFRACTION98.94
2.27-2.320.27421350.20072639X-RAY DIFFRACTION99.43
2.32-2.370.24341450.17812719X-RAY DIFFRACTION99.79
2.37-2.420.2251360.17682652X-RAY DIFFRACTION99.71
2.42-2.480.22131430.1592667X-RAY DIFFRACTION99.75
2.48-2.550.19031390.16112683X-RAY DIFFRACTION99.82
2.55-2.620.19441400.15982638X-RAY DIFFRACTION99.64
2.62-2.710.25011390.16022662X-RAY DIFFRACTION99.5
2.71-2.810.20581430.15622661X-RAY DIFFRACTION99.93
2.81-2.920.19231440.15742662X-RAY DIFFRACTION99.89
2.92-3.050.21651350.15862685X-RAY DIFFRACTION99.82
3.05-3.210.17271430.16622691X-RAY DIFFRACTION99.86
3.21-3.410.21451380.15682671X-RAY DIFFRACTION99.61
3.41-3.680.16531370.14382642X-RAY DIFFRACTION99.07
3.68-4.050.17261420.13522635X-RAY DIFFRACTION99.28
4.05-4.630.13911500.11052665X-RAY DIFFRACTION99.65
4.63-5.830.17551360.12632677X-RAY DIFFRACTION99.79
5.83-45.060.20031430.1812665X-RAY DIFFRACTION99.5
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)
15.306770475232.235120280680.04804446971993.38978572821-3.697414380218.859866356950.02111735602620.4607195892070.897320411836-0.438561465723-0.197400188569-0.150222812503-0.8787683984930.4182146142810.03590082509170.5308932913130.02707920123960.0855768562030.3100338863610.05334267101870.51342444685159.72910654159.098470332817.2033834205
20.9147511837190.6117009598550.001027137090312.680556883710.3070497155760.6855842161990.00130753851911-0.07581363001340.07485946811550.0553481306521-0.01443315625780.00335189694967-0.0849679038314-0.02565443064930.008275609752640.1798166772810.00654244846347-0.02034902370740.225054125829-0.003401118779990.19566451237952.108169128251.524487433943.5230890729
31.35204774424-0.348872648885-0.03296948293771.480468796450.1522128854272.015268006370.04357187282660.1223758852690.0003821054322-0.0768432468912-0.04037129358080.0349505538725-0.00567444786321-0.160969358810.00289498710830.191380642458-0.01239641201050.00580898600830.297736939034-0.002324913300960.22081389708556.926602193438.238064643419.4921591178
42.708244870980.3765190663520.5424765096042.91162143301-0.4024866846892.378795702210.05219489771370.0300959742264-0.2026185160710.06832107751270.002549560312750.1843646664150.16400706883-0.0055630275393-0.02621572111370.2077613276920.0170905461954-0.000468480265010.218206522515-0.02399603753630.26990084904857.409262965816.640849947741.5765547501
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 6 through 33 or resid 75 through 137 or resid 339 through 366)
4X-RAY DIFFRACTION4chain 'G' and resid 28 through 149

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