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- PDB-4cbx: Crystal structure of Plasmodium berghei actin II -

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Basic information

Entry
Database: PDB / ID: 4cbx
TitleCrystal structure of Plasmodium berghei actin II
Components
  • ACTIN-2
  • GELSOLIN
KeywordsMOTOR PROTEIN / MALARIA / MOTILITY / PARASITE
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 / 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 / Neutrophil degranulation / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to type II interferon / 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 / 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 / PHOSPHATE ION / Gelsolin / Actin-2
Similarity search - Component
Biological speciesPLASMODIUM BERGHEI (eukaryote)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVahokoski, J. / Bhargav, S.P. / Desfosses, A. / Andreadaki, M. / Kumpula, E.P. / Ignatev, A. / Munico Martinez, S. / Lepper, S. / Frischknecht, F. / Siden-Kiamos, I. ...Vahokoski, J. / Bhargav, S.P. / Desfosses, A. / Andreadaki, M. / Kumpula, E.P. / Ignatev, A. / Munico Martinez, S. / Lepper, S. / Frischknecht, F. / Siden-Kiamos, I. / Sachse, C. / Kursula, I.
CitationJournal: PLoS Pathog / Year: 2014
Title: Structural differences explain diverse functions of Plasmodium actins.
Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht ...Authors: Juha Vahokoski / Saligram Prabhakar Bhargav / Ambroise Desfosses / Maria Andreadaki / Esa-Pekka Kumpula / Silvia Muñico Martinez / Alexander Ignatev / Simone Lepper / Friedrich Frischknecht / Inga Sidén-Kiamos / Carsten Sachse / Inari Kursula /
Abstract: Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also ...Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties.
History
DepositionOct 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)58,00510
Polymers57,0682
Non-polymers9388
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-87.6 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.248, 60.908, 75.518
Angle α, β, γ (deg.)90.00, 97.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein ACTIN-2 / ACTIN II / ACTIN


Mass: 42856.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q4YU79
#2: Protein GELSOLIN / ACTIN-DEPOLYMERIZING FACTOR / ADF / BREVIN / GELSOLIN G1


Mass: 14211.929 Da / Num. of mol.: 1 / Fragment: G1 DOMAIN, RESIDUES 50-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: P13020

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Non-polymers , 6 types, 356 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6.5
Details: 18% (W/V) PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54
DetectorType: PLATINUM135 / Detector: CCD / Date: Aug 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→32 Å / Num. obs: 29458 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.62 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.6
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 0.9 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PROTEUM2data reduction
PROTEUM2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P8Z

1p8z


Resolution: 2.2→31.907 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1492 5.1 %
Rwork0.1959 --
obs0.1975 29435 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→31.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 50 348 4188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074112
X-RAY DIFFRACTIONf_angle_d0.675579
X-RAY DIFFRACTIONf_dihedral_angle_d12.4131526
X-RAY DIFFRACTIONf_chiral_restr0.05604
X-RAY DIFFRACTIONf_plane_restr0.003721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.27021540.25362410X-RAY DIFFRACTION95
2.271-2.35210.28781200.25322516X-RAY DIFFRACTION100
2.3521-2.44630.31251310.25932541X-RAY DIFFRACTION100
2.4463-2.55760.28191290.23682560X-RAY DIFFRACTION100
2.5576-2.69230.30911460.22992526X-RAY DIFFRACTION100
2.6923-2.86090.24271180.21692548X-RAY DIFFRACTION100
2.8609-3.08170.23891160.22012573X-RAY DIFFRACTION100
3.0817-3.39150.24571270.20752579X-RAY DIFFRACTION100
3.3915-3.88150.21961360.17442530X-RAY DIFFRACTION100
3.8815-4.88740.17881700.14242538X-RAY DIFFRACTION100
4.8874-31.91030.17371450.16232622X-RAY DIFFRACTION100
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)
10.38280.0061-0.1560.37110.02980.06590.0992-0.36790.04140.42350.0249-0.12890.079-0.02620.17430.36810.143-0.09770.3544-0.04380.004934.6716-6.016730.8175
20.03270.0131-0.00690.021-0.07010.13510.0472-0.07360.09950.17770.038-0.06370.19630.1288-0.00190.24750.096-0.02220.2411-0.00650.194233.5824-12.925724.3882
30.0853-0.15070.03360.1948-0.01970.0164-0.0319-0.1722-0.04470.03890.0643-0.1205-0.03520.023-0.00040.17610.0473-0.00850.1622-0.01610.200633.9879-3.405519.3896
40.00990.02260.02720.13460.03930.1076-0.055-0.10670.04630.0840.0544-0.01250.0990.0456-00.17460.0384-0.00640.1859-0.01440.175935.7554-15.923717.4355
50.04760.2249-0.02641.01750.05280.6197-0.0483-0.06880.11390.07370.01450.17910.0122-0.1475-00.13180.04630.02340.1664-0.01250.14292.95337.475118.9993
60.68520.255-0.06860.76740.02270.4144-0.12270.05450.0544-0.1140.04320.0530.00110.0055-0.18860.1014-0.0204-0.00890.07740.00350.098813.48614.269-3.6585
70.0079-0.0227-0.00640.040.0063-0.0018-0.1342-0.17750.0527-0.1776-0.05270.1545-0.21610.2472-0.00060.50190.0843-0.03480.4182-0.0580.278616.14359.352432.1045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN G AND (RESID 28 THROUGH 46 )
2X-RAY DIFFRACTION2CHAIN G AND (RESID 47 THROUGH 75 )
3X-RAY DIFFRACTION3CHAIN G AND (RESID 76 THROUGH 127 )
4X-RAY DIFFRACTION4CHAIN G AND (RESID 128 THROUGH 149 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 5 THROUGH 144 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 145 THROUGH 349 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 350 THROUGH 373 )

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