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- PDB-4cbw: Crystal structure of Plasmodium berghei actin I with D-loop from ... -

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Basic information

Entry
Database: PDB / ID: 4cbw
TitleCrystal structure of Plasmodium berghei actin I with D-loop from muscle actin
Components
  • ACTIN, ALPHA SKELETAL MUSCLE, ACTIN
  • GELSOLIN
KeywordsMOTOR PROTEIN / MALARIA / MOTILITY / PARASITE
Function / homology
Function and homology information


glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / 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 ...glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / 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 / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / positive regulation of p38MAPK cascade / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / positive regulation of cardiac muscle hypertrophy / hepatocyte apoptotic process / cilium assembly / sarcoplasm / phagocytic vesicle / vesicle-mediated transport / ruffle / cellular response to cadmium ion / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / Neutrophil degranulation / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / myelin sheath / actin binding / actin cytoskeleton organization / amyloid fibril formation / cytoskeleton / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / protein-containing complex / 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 / 1,4-DIETHYLENE DIOXIDE / Gelsolin / Actin-1
Similarity search - Component
Biological speciesPLASMODIUM BERGHEI (eukaryote)
SYNTHETIC CONSTRUCT (others)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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 1.1May 14, 2014Group: Data collection
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Dec 20, 2023Group: 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 / struct_site
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 / _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, ALPHA SKELETAL MUSCLE, ACTIN
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8727
Polymers56,1562
Non-polymers7165
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-45.1 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.240, 69.530, 178.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein ACTIN, ALPHA SKELETAL MUSCLE, ACTIN / / ACTIN I / ALPHA-ACTIN-1 / ACTIN


Mass: 41944.480 Da / Num. of mol.: 1
Fragment: ACTIN RESIDUES 2-39, ALPHA SKELETAL MUSCLE RESIDUES 40-61,
Source method: isolated from a genetically manipulated source
Details: RESIDUES 40-61 REPLACED BY THOSE OF SKELETAL MUSCLE ACTIN
Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote), (gene. exp.) SYNTHETIC CONSTRUCT (others)
Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: Q4Z1L3
#2: Protein GELSOLIN / / ACTIN-DEPOLYMERIZING FACTOR / ADF / BREVIN / GELSOLIN G1


Mass: 14211.929 Da / Num. of mol.: 1 / Fragment: G1 DOMAIN, RESIDUES 25-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P13020

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Non-polymers , 4 types, 61 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 8
Details: 100 MM TRIS-HCL (PH 8.0), 8% (W/V), PEG 20000, 2% (V/V) DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→38.5 Å / Num. obs: 24163 / % possible obs: 99.6 % / Observed criterion σ(I): -1 / Redundancy: 6.7 % / Biso Wilson estimate: 55.19 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.9 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CBU

4cbu


Resolution: 2.501→38.581 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 32.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1205 5 %
Rwork0.2107 --
obs0.2134 24077 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75 Å2
Refinement stepCycle: LAST / Resolution: 2.501→38.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 40 56 3956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033987
X-RAY DIFFRACTIONf_angle_d0.685399
X-RAY DIFFRACTIONf_dihedral_angle_d13.4871479
X-RAY DIFFRACTIONf_chiral_restr0.041580
X-RAY DIFFRACTIONf_plane_restr0.002696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5009-2.60110.45911260.4122454X-RAY DIFFRACTION98
2.6011-2.71940.36961390.34082485X-RAY DIFFRACTION100
2.7194-2.86270.31841300.29162519X-RAY DIFFRACTION100
2.8627-3.0420.29541290.25672517X-RAY DIFFRACTION100
3.042-3.27680.35891350.25652502X-RAY DIFFRACTION100
3.2768-3.60630.26821300.21312543X-RAY DIFFRACTION100
3.6063-4.12770.3011350.19062553X-RAY DIFFRACTION100
4.1277-5.19840.18151370.16482577X-RAY DIFFRACTION100
5.1984-38.58510.22111440.17232722X-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)
10.97310.0904-0.73453.4619-0.49127.85220.13050.07550.2690.43850.0940.1378-0.2213-0.5055-0.2070.36710.1168-0.00490.5973-0.12620.8663-19.70091.6653-18.109
21.02180.99940.09782.41440.34161.48280.0263-0.28560.00330.343-0.07940.3528-0.0166-0.13080.05160.32590.01830.02550.4911-0.07970.7616-8.6987-2.0718-19.7584
32.27240.8021-0.67213.11772.49064.57330.0844-0.43090.04560.27650.1988-0.2597-0.16690.6084-0.26160.3846-0.0307-0.10640.6167-0.1130.74816.320214.1867-18.3872
40.03530.5119-0.23999.0771-3.16261.50850.035-0.10280.2646-0.433-0.07630.57830.4341-0.22230.18080.36020.02610.08130.5226-0.14560.939-12.8612-11.6553-33.7653
54.8095.74955.67926.87386.78946.70690.2884-1.1746-1.21360.4532-0.99471.52631.0191-1.92070.56030.4599-0.1059-0.00330.6487-0.01541.2519-10.1844-11.3435-52.408
62.908-2.252-1.26283.8162-2.27765.7609-0.2881.2978-1.0773-0.9449-0.27531.08230.7074-0.48860.49270.5044-0.09240.04810.6091-0.08780.9008-2.3854-5.2583-57.0133
77.7181-0.0747-7.16036.53121.51947.7301-0.2565-0.0117-0.6587-0.7826-0.16980.5923-0.2077-1.23180.27340.2368-0.0172-0.09140.5779-0.09520.9207-10.06991.7673-55.1189
83.46050.2291-1.91741.6381.76064.9423-0.09210.35790.0938-0.4073-0.0310.0799-0.2881-0.34960.12680.3133-0.0133-0.01180.42850.08880.9055-0.36472.2699-55.7634
93.4398-3.6118-3.86353.81574.26986.56910.02540.0137-0.41620.04420.2774-1.00330.23580.2086-0.27030.3051-0.0287-0.02410.2829-0.02881.03384.3383-2.9314-51.5551
106.1165-3.7916-1.87447.45472.06122.71270.0897-0.4302-0.62080.45250.18690.36230.41020.1053-0.29830.3597-0.0452-0.08480.46670.03530.435-4.268-2.8643-43.9358
113.9641.1885-1.61943.0608-2.21933.7967-0.2363-0.25140.2298-0.98420.1487-1.0594-0.0495-0.01410.13910.4026-0.06610.0730.3805-0.02830.87196.93710.6868-49.8863
128.1579-1.7598-3.11085.6004-3.77865.0639-0.26651.5229-0.6635-0.4336-0.04780.6987-0.1395-0.1070.23750.5228-0.0469-0.10620.5799-0.11880.4843.36839.8013-60.6612
138.21822.1976-4.06823.9529-3.60738.42130.87340.1371-0.1376-0.0992-0.19771.0654-0.7897-0.7759-0.47450.56220.10730.05920.4987-0.08631.2976-12.136911.5879-47.7292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 7 THROUGH 57 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 58 THROUGH 199 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 200 THROUGH 340 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 341 THROUGH 378 )
5X-RAY DIFFRACTION5CHAIN G AND (RESID 27 THROUGH 34 )
6X-RAY DIFFRACTION6CHAIN G AND (RESID 35 THROUGH 46 )
7X-RAY DIFFRACTION7CHAIN G AND (RESID 47 THROUGH 58 )
8X-RAY DIFFRACTION8CHAIN G AND (RESID 59 THROUGH 75 )
9X-RAY DIFFRACTION9CHAIN G AND (RESID 76 THROUGH 94 )
10X-RAY DIFFRACTION10CHAIN G AND (RESID 95 THROUGH 111 )
11X-RAY DIFFRACTION11CHAIN G AND (RESID 112 THROUGH 133 )
12X-RAY DIFFRACTION12CHAIN G AND (RESID 134 THROUGH 141 )
13X-RAY DIFFRACTION13CHAIN G AND (RESID 142 THROUGH 149 )

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