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- PDB-6i4j: Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) ... -

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Basic information

Entry
Database: PDB / ID: 6i4j
TitleCrystal Structure of Plasmodium falciparum actin I (F54Y mutant) in the Mg-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 / : / 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: 1.5 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_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)57,34613
Polymers56,2762
Non-polymers1,07011
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-59 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.560, 71.350, 109.670
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-781-

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, 524 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-MG / MAGNESIUM ION


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


Mass: 58.082 Da / Num. of mol.: 5 / 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#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.: 513 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
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: I04-1 / Wavelength: 1.137 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.137 Å / Relative weight: 1
ReflectionResolution: 1.5→45.07 Å / Num. obs: 162244 / % possible obs: 97.44 % / Redundancy: 2.7 % / Biso Wilson estimate: 20.71 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06987 / Rpim(I) all: 0.04726 / Rrim(I) all: 0.08476 / Net I/σ(I): 7.77
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.938 / Num. unique obs: 15884 / CC1/2: 0.401 / Rpim(I) all: 0.7018 / Rrim(I) all: 1.178 / % possible all: 95.06

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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→45.07 Å / SU ML: 0.1954 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 21.3712
RfactorNum. reflection% reflection
Rfree0.1978 8135 5.01 %
Rwork0.1646 --
obs0.1663 162232 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 60 513 4259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214310
X-RAY DIFFRACTIONf_angle_d1.21655875
X-RAY DIFFRACTIONf_chiral_restr0.0879626
X-RAY DIFFRACTIONf_plane_restr0.0083773
X-RAY DIFFRACTIONf_dihedral_angle_d14.31181632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.34782700.34255065X-RAY DIFFRACTION95.83
1.52-1.530.33512590.31884880X-RAY DIFFRACTION93.66
1.53-1.550.30922650.29735128X-RAY DIFFRACTION95.42
1.55-1.570.33962740.29385108X-RAY DIFFRACTION97.66
1.57-1.590.29882700.28655178X-RAY DIFFRACTION97.76
1.59-1.620.29192720.28515135X-RAY DIFFRACTION97.55
1.62-1.640.31922680.27865128X-RAY DIFFRACTION98.07
1.64-1.660.31032730.27135154X-RAY DIFFRACTION97.78
1.66-1.690.26912710.25455165X-RAY DIFFRACTION97.58
1.69-1.720.28162780.24855141X-RAY DIFFRACTION97.34
1.72-1.750.24022700.24395055X-RAY DIFFRACTION96.75
1.75-1.780.25632670.24084960X-RAY DIFFRACTION93.94
1.78-1.810.26742670.22175001X-RAY DIFFRACTION95.26
1.81-1.850.27922770.21455154X-RAY DIFFRACTION97.59
1.85-1.890.24062690.19665157X-RAY DIFFRACTION97.84
1.89-1.930.21932730.1835159X-RAY DIFFRACTION97.57
1.93-1.980.21512700.17445142X-RAY DIFFRACTION97.48
1.98-2.040.21472760.16845148X-RAY DIFFRACTION97.91
2.04-2.10.19272680.16585172X-RAY DIFFRACTION97.68
2.1-2.160.19122690.15625091X-RAY DIFFRACTION97.05
2.16-2.240.16222650.14634942X-RAY DIFFRACTION93.75
2.24-2.330.18482710.13955138X-RAY DIFFRACTION97.99
2.33-2.440.18032800.14035246X-RAY DIFFRACTION98.98
2.44-2.560.17692770.13285235X-RAY DIFFRACTION99.35
2.56-2.730.17192690.13515241X-RAY DIFFRACTION99.3
2.73-2.940.1752710.13925199X-RAY DIFFRACTION98.79
2.94-3.230.1842720.15265219X-RAY DIFFRACTION98.65
3.23-3.70.17652730.14335246X-RAY DIFFRACTION99.41
3.7-4.660.14822760.11715247X-RAY DIFFRACTION99.77
4.66-45.090.18932750.16485263X-RAY DIFFRACTION99.48
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)
10.00501149271346-0.004673419217550.002538880333250.001877498639220.0002278495381290.00293180909167-0.02566743787250.003084977013090.09173950329720.0730951078613-0.01994035044910.0312083016066-0.0962644421210.03403205423281.30192511102E-50.3352290473020.001411522378440.0002935478673470.192287495397-0.06874877632140.29051662607878.916478385893.7890775376255.615461697
20.1417522164150.003583129376140.03318271052760.16600488512-0.05642554053040.163787904529-0.02331847796860.08923969038770.0344235228984-0.07941800340030.03088585066530.0107655246881-0.09664216429480.09474541385150.05765188678820.05609691665430.00905175326103-0.02079371873090.008274846975850.02833766401930.031345543665685.330088089886.7675424051231.110614574
30.06687870036290.0183792134642-0.0460299578130.04812839724820.002083497120340.110354512495-0.00990986954869-0.102232030922-0.00469485730780.04875371244050.0120552503259-0.00379282621180.00302202911250.0926850727171-1.65153278235E-50.1998317652180.001068905385210.001876549169290.2681209055030.005703609747790.19804451534680.483432119273.4381298557254.792785651
40.05230112980320.05927917088310.04581955939860.08755487480820.006947512656630.09132485428390.0549888155741-0.0209180865944-0.131290293589-0.069332891778-0.0334084676727-0.09142802471560.0934129709822-0.0357955266158-0.0004144457582870.1426504883840.00131052448388-0.01474901206470.1109892882620.01236965501820.15662064999378.745878777952.9247669696232.282609697
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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