[English] 日本語
Yorodumi
- PDB-4cbu: Crystal structure of Plasmodium falciparum actin I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cbu
TitleCrystal structure of Plasmodium falciparum actin I
Components
  • Actin-1
  • Gelsolin
KeywordsMOTOR PROTEIN / MALARIA / MOTILITY / PARASITE
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 / hydrolase activity / 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 / Gelsolin / Actin-1 / Actin-1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
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 / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _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_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin-1
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8876
Polymers56,2602
Non-polymers6274
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-52.4 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.980, 110.300, 71.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2390-

HOH

21A-2680-

HOH

31A-2721-

HOH

41A-2760-

HOH

51G-2650-

HOH

-
Components

#1: Protein Actin-1 / PfAct1 / Actin I / PfActI


Mass: 42047.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ACT1, ACTI, PF3D7_1246200, PFL2215w / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21
References: UniProt: Q8I4X0, UniProt: P86287*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Gelsolin / Actin-depolymerizing factor / ADF / Brevin


Mass: 14211.929 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsn, Gsb / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P13020
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6.5
Details: 22%(W/V) PEG 3350, 0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS-TRIS PROPANE PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→55 Å / Num. obs: 134201 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 10.69 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.65 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→55.15 Å / SU ML: 0.11 / σ(F): 1.99 / Phase error: 13.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1534 4040 3 %
Rwork0.1205 --
obs0.1215 134194 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.96 Å2
Refinement stepCycle: LAST / Resolution: 1.3→55.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 34 774 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124589
X-RAY DIFFRACTIONf_angle_d1.4816301
X-RAY DIFFRACTIONf_dihedral_angle_d14.5711767
X-RAY DIFFRACTIONf_chiral_restr0.098660
X-RAY DIFFRACTIONf_plane_restr0.009850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31530.26241500.25024318X-RAY DIFFRACTION98
1.3153-1.33130.25151250.22444424X-RAY DIFFRACTION100
1.3313-1.34820.27011280.21044492X-RAY DIFFRACTION100
1.3482-1.36590.23131350.19164398X-RAY DIFFRACTION100
1.3659-1.38470.20971450.18314465X-RAY DIFFRACTION100
1.3847-1.40440.20491410.16214450X-RAY DIFFRACTION100
1.4044-1.42540.21541230.15154458X-RAY DIFFRACTION100
1.4254-1.44770.19621440.14414451X-RAY DIFFRACTION100
1.4477-1.47140.15941310.13144460X-RAY DIFFRACTION100
1.4714-1.49680.16991500.12144458X-RAY DIFFRACTION100
1.4968-1.5240.16741300.11464459X-RAY DIFFRACTION100
1.524-1.55330.14991570.10834437X-RAY DIFFRACTION100
1.5533-1.5850.15281340.10114466X-RAY DIFFRACTION100
1.585-1.61950.13651360.09924464X-RAY DIFFRACTION100
1.6195-1.65720.13971230.09494490X-RAY DIFFRACTION100
1.6572-1.69860.13571400.08874448X-RAY DIFFRACTION100
1.6986-1.74450.14471380.08914510X-RAY DIFFRACTION100
1.7445-1.79590.13031380.09064431X-RAY DIFFRACTION100
1.7959-1.85390.11451300.08834518X-RAY DIFFRACTION100
1.8539-1.92010.12441280.09024500X-RAY DIFFRACTION100
1.9201-1.9970.12971400.08924485X-RAY DIFFRACTION100
1.997-2.08790.12821190.08974537X-RAY DIFFRACTION100
2.0879-2.1980.11551570.09744484X-RAY DIFFRACTION100
2.198-2.33570.12471490.09854502X-RAY DIFFRACTION100
2.3357-2.5160.14781330.10424547X-RAY DIFFRACTION100
2.516-2.76920.13611470.11714547X-RAY DIFFRACTION100
2.7692-3.16990.15141510.12784571X-RAY DIFFRACTION100
3.1699-3.99360.1481560.12514598X-RAY DIFFRACTION100
3.9936-55.19970.17951620.15064786X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more