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- PDB-6i4h: Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) ... -

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Basic information

Entry
Database: PDB / ID: 6i4h
TitleCrystal Structure of Plasmodium falciparum actin I (F54Y 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 / Caspase-mediated cleavage of cytoskeletal proteins / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / 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 / Caspase-mediated cleavage of cytoskeletal proteins / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / 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 depolymerization / actin filament capping / cardiac muscle cell contraction / podosome / relaxation of cardiac muscle / phagocytosis, engulfment / hepatocyte apoptotic process / sarcoplasm / cilium assembly / vesicle-mediated transport / phagocytic vesicle / response to muscle stretch / actin filament polymerization / cytoskeleton organization / Neutrophil degranulation / actin filament / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cellular response to type II interferon / 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 / 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 / DI(HYDROXYETHYL)ETHER / Gelsolin / Actin-1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)57,0458
Polymers56,2762
Non-polymers7696
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-56 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.870, 71.540, 110.600
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-807-

HOH

21A-998-

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 , 5 types, 686 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 680 / 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: 49.06 %
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: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.4→43.75 Å / Num. obs: 206841 / % possible obs: 99.45 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05007 / Rpim(I) all: 0.03227 / Rrim(I) all: 0.05975 / Net I/σ(I): 12.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.98 / Num. unique obs: 20505 / CC1/2: 0.398 / Rpim(I) all: 0.633 / Rrim(I) all: 1.171 / % possible all: 99.03

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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: 1.4→43.75 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 0.89 / Phase error: 16.7453
RfactorNum. reflection% reflection
Rfree0.1632 10319 4.99 %
Rwork0.1426 --
obs0.1437 206795 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.61 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 42 680 4443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094340
X-RAY DIFFRACTIONf_angle_d1.15245959
X-RAY DIFFRACTIONf_chiral_restr0.0785644
X-RAY DIFFRACTIONf_plane_restr0.007786
X-RAY DIFFRACTIONf_dihedral_angle_d18.81161673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.35713420.32126451X-RAY DIFFRACTION98.51
1.42-1.430.33673410.29316527X-RAY DIFFRACTION99.11
1.43-1.450.31273410.28076494X-RAY DIFFRACTION99.14
1.45-1.470.26213460.25366553X-RAY DIFFRACTION99.02
1.47-1.490.23853470.23516545X-RAY DIFFRACTION99.45
1.49-1.510.27343410.22616478X-RAY DIFFRACTION98.97
1.51-1.530.23943460.20936540X-RAY DIFFRACTION99.06
1.53-1.550.22213480.19966580X-RAY DIFFRACTION99.17
1.55-1.580.23363340.19966479X-RAY DIFFRACTION99.21
1.58-1.60.21153460.18146624X-RAY DIFFRACTION99.54
1.6-1.630.20843500.17236542X-RAY DIFFRACTION99.34
1.63-1.660.1953430.16316455X-RAY DIFFRACTION99.5
1.66-1.690.19223480.15726596X-RAY DIFFRACTION99.47
1.69-1.730.19043390.15356580X-RAY DIFFRACTION99.41
1.73-1.760.17083410.14196557X-RAY DIFFRACTION99.7
1.76-1.80.15873490.14236585X-RAY DIFFRACTION99.43
1.8-1.850.16433410.13886521X-RAY DIFFRACTION99.56
1.85-1.90.15713410.13876525X-RAY DIFFRACTION99.39
1.9-1.960.1563420.13696599X-RAY DIFFRACTION99.76
1.96-2.020.15673470.13636551X-RAY DIFFRACTION99.74
2.02-2.090.15483500.13336607X-RAY DIFFRACTION99.58
2.09-2.170.15553390.12616508X-RAY DIFFRACTION99.52
2.17-2.270.16463470.12946575X-RAY DIFFRACTION99.78
2.27-2.390.16373500.12736608X-RAY DIFFRACTION99.8
2.39-2.540.15743450.12576558X-RAY DIFFRACTION99.62
2.54-2.740.14423370.12396540X-RAY DIFFRACTION99.65
2.74-3.020.14743450.12736581X-RAY DIFFRACTION99.76
3.02-3.450.12933510.13136587X-RAY DIFFRACTION99.73
3.45-4.350.14183450.12296542X-RAY DIFFRACTION99.61
4.35-45.290.15673370.14666588X-RAY DIFFRACTION99.76
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)
12.5280379077-1.50502122261.11566285292.980824673031.37698333342.853567132070.214443087037-0.5183097942760.8337260846440.526599804908-0.06081905036320.369189250286-0.913325736767-0.370484177080.1414480171740.468576938944-0.01163313006510.1173096489220.281918645438-0.09998625412410.37954964682978.252576009194.6000670571258.355687863
20.742575617061-0.326904570674-0.05500064442221.75271543405-0.3430214880820.632995702061-0.01398848308310.05643559294040.126987507937-0.04147910620570.02986725863120.0634119275571-0.130901417412-0.0125970751544-0.007906949837680.135550814078-0.00251517757673-0.02499711608350.1388535490250.005234183928530.12803205203385.267897887587.1643104384232.480422032
30.822899622640.206431073057-0.2757448651030.93718221284-0.1231232088311.822563817170.00443994833407-0.130284406155-0.02915411915870.0652573347439-0.03764939833120.005041251283860.008288982257320.1271345880570.02922018257520.1016922272560.002596709128410.0008894867870790.1747488467040.007942782725380.1207284238180.563983955773.9228819929256.641076345
41.566188394780.5053498036020.4648254956641.368964443420.2954583932761.411527922510.0620856495704-0.0157383707358-0.237598311966-0.0220869000252-0.00616386092588-0.1829831314070.1387477029130.02558951028490.005445298197310.1110189283140.0103962907425-0.009419924161360.08504659007650.01464167521360.13451840507678.993272585452.9043350059234.193986944
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 4 through 125

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