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- PDB-6i4f: Crystal Structure of Plasmodium falciparum actin I (A272W mutant)... -

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Basic information

Entry
Database: PDB / ID: 6i4f
TitleCrystal Structure of Plasmodium falciparum actin I (A272W 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 / 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'-DIPHOSPHATE / 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: 1.5 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)57,82612
Polymers56,3752
Non-polymers1,45210
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-70 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.760, 71.450, 110.040
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-755-

HOH

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Actin-1 / Actin I


Mass: 42162.809 Da / Num. of mol.: 1 / Mutation: A272W
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 , 10 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-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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#12: 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 11% PEG3350, 0.1 M BIS-TRIS pH 5.8, 0.2M K-SCN; streak seeded; 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: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.5→45.18 Å / Num. obs: 167763 / % possible obs: 99.99 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09478 / Rpim(I) all: 0.03958 / Rrim(I) all: 0.1028 / Net I/σ(I): 10.71
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.123 / Num. unique obs: 16758 / CC1/2: 0.365 / Rpim(I) all: 0.8832 / Rrim(I) all: 2.301 / % possible all: 99.99

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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: 1.5→45.18 Å / SU ML: 0.1982 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 20.006
RfactorNum. reflection% reflection
Rfree0.1921 2175 1.3 %
Rwork0.1555 --
obs0.156 167756 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.99 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 85 517 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934214
X-RAY DIFFRACTIONf_angle_d1.02865765
X-RAY DIFFRACTIONf_chiral_restr0.0579617
X-RAY DIFFRACTIONf_plane_restr0.007741
X-RAY DIFFRACTIONf_dihedral_angle_d11.70532563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.33691220.304810382X-RAY DIFFRACTION100
1.53-1.570.27651410.281110345X-RAY DIFFRACTION99.98
1.57-1.610.31351360.279510312X-RAY DIFFRACTION100
1.61-1.650.30821420.276810346X-RAY DIFFRACTION99.99
1.65-1.70.26921240.243710368X-RAY DIFFRACTION99.99
1.7-1.750.23881410.223110315X-RAY DIFFRACTION99.98
1.75-1.820.21931400.196310349X-RAY DIFFRACTION99.94
1.82-1.890.2421330.17810366X-RAY DIFFRACTION100
1.89-1.980.19811410.171110348X-RAY DIFFRACTION99.99
1.98-2.080.2021400.149210347X-RAY DIFFRACTION99.98
2.08-2.210.1741370.141810378X-RAY DIFFRACTION100
2.21-2.380.1841340.135510355X-RAY DIFFRACTION100
2.38-2.620.17751380.134210324X-RAY DIFFRACTION100
2.62-30.17761340.140410338X-RAY DIFFRACTION100
3-3.780.18861430.139910363X-RAY DIFFRACTION100
3.78-45.20.15451290.135410345X-RAY DIFFRACTION99.96
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)
10.2136483074860.02830444469930.008096407495320.384186827237-0.4136461125980.4508987590230.0938526331432-0.2206002968390.7520902800430.561085058695-0.02373769616920.225092382502-0.806434566061-0.09761870294460.009284975494730.596418348581-0.008364349531780.02811346008950.327473832987-0.08223869907450.44250130224110.35150570122.3691004575256.017324448
20.689914764446-0.632385733846-0.01032228121452.08788139013-0.4920321777870.448162212396-0.01777459329130.02730398293670.0842667300323-0.02384251277360.0425394660530.0107670615312-0.08366922522190.005673785710210.0001527477791890.167850525921-0.00830265973898-0.02031980904780.1657940522750.0002130617114220.15579276406416.337026035315.4819725101231.367516497
30.9413652136120.251165699368-0.2669381509320.673116910473-0.04991730222611.59967559648-0.0214043672897-0.166285718757-0.05220308090870.0426374603333-0.00439019974168-0.04641562203860.01508899645540.2329161013068.55386582334E-50.1620873931320.0023979689106-0.0008414058381720.2609346175260.01487780984080.18219360050413.8226707691.65878753371256.967873823
41.398279065850.3771112153240.4166992287871.506638164390.242323574141.45247410760.0639122745544-0.0530632656632-0.210547120019-0.00251604080069-0.0140271865241-0.1724864348510.1528268979450.04226076568140.01957973214110.1644278895450.00781948810073-0.008614683140170.1436709107950.0158611969160.18642980763111.038825558-19.0396171893233.305818337
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 370)
4X-RAY DIFFRACTION4chain 'G' and resid 26 through 149

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