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- PDB-6i4m: Crystal Structure of Plasmodium berghei actin II in the Mg-ADP state -

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Basic information

Entry
Database: PDB / ID: 6i4m
TitleCrystal Structure of Plasmodium berghei actin II in the Mg-ADP state
Components
  • Actin-2
  • Gelsolin
KeywordsCONTRACTILE PROTEIN / hydrolase / filamentous / cytoskeleton
Function / homology
Function and homology information


positive regulation of development of symbiont in host / exit from host cell / male gamete generation / Caspase-mediated cleavage of cytoskeletal proteins / 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 development of symbiont in host / exit from host cell / male gamete generation / Caspase-mediated cleavage of cytoskeletal proteins / 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 / regulation of podosome assembly / cilium organization / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / actin filament depolymerization / actin filament capping / 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 / protein destabilization / cellular response to type II interferon / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / lamellipodium / actin cytoskeleton organization / amyloid fibril formation / cytoskeleton / 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-2
Similarity search - Component
Biological speciesPlasmodium berghei (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.873 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-2
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6438
Polymers56,9952
Non-polymers6486
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-63 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.410, 61.510, 64.940
Angle α, β, γ (deg.)90.000, 92.548, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Actin-2 / Actin II


Mass: 42869.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (strain Anka) (eukaryote)
Strain: Anka / Gene: PB001050.02.0 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4YU79
#2: Protein Gelsolin / Actin-depolymerizing factor / ADF / Brevin


Mass: 14125.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GP results from cleavage with 3C protease
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, 450 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.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 23% PEG3350, 0.1M BIS-TRIS pH 6.3, 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.031 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.031 Å / Relative weight: 1
ReflectionResolution: 1.873→64.88 Å / Num. obs: 73248 / % possible obs: 93.81 % / Redundancy: 1.9 % / Biso Wilson estimate: 22.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03798 / Rpim(I) all: 0.03352 / Rrim(I) all: 0.05083 / Net I/σ(I): 15.1
Reflection shellResolution: 1.873→1.94 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2955 / Num. unique obs: 4975 / CC1/2: 0.826 / Rpim(I) all: 0.2727 / Rrim(I) all: 0.4032 / % possible all: 63.77

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBX

4cbx


Resolution: 1.873→64.88 Å / SU ML: 0.1579 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 17.1608
RfactorNum. reflection% reflection
Rfree0.1788 3555 4.85 %
Rwork0.1428 --
obs0.1446 73246 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.78 Å2
Refinement stepCycle: LAST / Resolution: 1.873→64.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 36 444 4327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054094
X-RAY DIFFRACTIONf_angle_d1.08035566
X-RAY DIFFRACTIONf_chiral_restr0.0573602
X-RAY DIFFRACTIONf_plane_restr0.0068720
X-RAY DIFFRACTIONf_dihedral_angle_d11.53362452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.2747530.25611271X-RAY DIFFRACTION42.68
1.9-1.930.25611360.22412237X-RAY DIFFRACTION75.36
1.93-1.950.23171270.1962516X-RAY DIFFRACTION85.7
1.95-1.990.28651340.18512999X-RAY DIFFRACTION98.06
1.99-2.020.22091420.17252897X-RAY DIFFRACTION98.32
2.02-2.050.18641370.16382973X-RAY DIFFRACTION98.6
2.05-2.090.16081390.16542861X-RAY DIFFRACTION97.82
2.09-2.130.21051500.16062936X-RAY DIFFRACTION97.41
2.13-2.170.18451480.15422873X-RAY DIFFRACTION96.27
2.17-2.220.231300.14892749X-RAY DIFFRACTION93.96
2.22-2.270.20041590.14492754X-RAY DIFFRACTION92.56
2.27-2.330.16181290.13972946X-RAY DIFFRACTION98.87
2.33-2.390.1681700.1282910X-RAY DIFFRACTION99.1
2.39-2.460.17731330.12622916X-RAY DIFFRACTION98.04
2.46-2.540.14821460.13262975X-RAY DIFFRACTION98.45
2.54-2.630.18631480.14162869X-RAY DIFFRACTION97.26
2.63-2.740.18891270.14432765X-RAY DIFFRACTION92.72
2.74-2.860.19471580.14772882X-RAY DIFFRACTION98.13
2.86-3.010.17651790.14132929X-RAY DIFFRACTION99.2
3.01-3.20.17961540.14712956X-RAY DIFFRACTION98.95
3.2-3.450.18311370.13562895X-RAY DIFFRACTION97.09
3.45-3.80.12541370.12812885X-RAY DIFFRACTION96.46
3.8-4.350.17591640.11812942X-RAY DIFFRACTION99.36
4.35-5.480.15741680.12082842X-RAY DIFFRACTION96.63
5.48-64.910.18851500.16242913X-RAY DIFFRACTION98.11
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)
11.63648116829-0.2050272200870.03177401088421.77416493337-0.1026500933971.60781904124-0.0909264174714-0.1445174992540.01812580872830.3128350003970.0527032781369-0.1254589754330.09094555752750.2752812528550.03384479275490.2306867049030.0832205194973-0.03306493043730.2300124830550.001335170822070.163942370865152.06380106-11.740023079687.2796384264
23.77926879174-0.2339326043541.106385095162.11140464462-0.4721555504511.39443342404-0.1943379999650.3859187093510.272344331813-0.1372218061760.1457734372331.20193338306-0.127290395845-1.067274340720.0379288554620.2926466633640.0657211770087-0.02663884800780.622853961852-0.0399528238090.55761844824111.7641907018.8845502549473.7961066423
31.485983986160.3818572728280.4201618747311.218977260060.1569139481131.30370710928-0.1527981911270.1610372425780.0831491882262-0.1415966357490.03319845036010.0276759081591-0.01802290412890.04799840488770.1048850829210.150755205607-0.01715756800510.01870883230010.139384415260.02088883910560.136092405722132.956890611.5845565562460.5480565376
41.53027349522-0.2909993528860.06034628426811.661642000620.01473207399882.86139975537-0.111123936218-0.1893868446370.03081818077540.307199095650.02579748648850.143973619254-0.0748875987327-0.1957577106020.08699699583930.2261503850370.03785126674220.04809574386840.2117587935560.002056145923290.184224886439127.0739731344.2495224365188.3325102703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 3 through 125)
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 73)
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 337)
4X-RAY DIFFRACTION4chain 'A' and (resid 6 through 32 or resid 74 through 136 or resid 338 through 376)

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