[English] 日本語
Yorodumi
- PDB-1dej: CRYSTAL STRUCTURE OF A DICTYOSTELIUM/TETRAHYMENA CHIMERA ACTIN (M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dej
TitleCRYSTAL STRUCTURE OF A DICTYOSTELIUM/TETRAHYMENA CHIMERA ACTIN (MUTANT 646: Q228K/T229A/A230Y/A231K/S232E/E360H) IN COMPLEX WITH HUMAN GELSOLIN SEGMENT 1
Components
  • CHIMERIC ACTIN
  • GELSOLIN
KeywordsCONTRACTILE PROTEIN / ACTIN MUTANT
Function / homology
Function and homology information


intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption ...intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / 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 / cell pole / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / plasma membrane repair / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / cell projection assembly / actin polymerization or depolymerization / early phagosome / cardiac muscle cell contraction / hyperosmotic response / relaxation of cardiac muscle / Sensory processing of sound by outer hair cells of the cochlea / podosome / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / myosin binding / pseudopodium / cell leading edge / mitotic cytokinesis / sarcoplasm / endocytic vesicle / cilium assembly / response to cAMP / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / phagocytic cup / vesicle-mediated transport / phagocytic vesicle / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / lipid droplet / actin filament organization / central nervous system development / 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 / endocytosis / cell morphogenesis / chemotaxis / actin filament binding / cell-cell junction / lamellipodium / actin cytoskeleton / actin binding / cell cortex / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / hydrolase activity / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / ATP binding / 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'-TRIPHOSPHATE / Gelsolin / Major actin
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
Tetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMatsuura, Y. / Stewart, M. / Kawamoto, M. / Kamiya, N. / Saeki, K. / Yasunaga, T. / Wakabayashi, T.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structural basis for the higher Ca(2+)-activation of the regulated actin-activated myosin ATPase observed with Dictyostelium/Tetrahymena actin chimeras.
Authors: Matsuura, Y. / Stewart, M. / Kawamoto, M. / Kamiya, N. / Saeki, K. / Yasunaga, T. / Wakabayashi, T.
#1: Journal: Nature / Year: 1993
Title: Structure of Gelsolin Segment 1-Actin Complex and the Mechanism of Filament Severing
Authors: Mclaughlin, P.J. / Gooch, J.T. / Mannherz, H.G. / Weeds, A.G.
#2: Journal: Biochemistry / Year: 1996
Title: Tropomyosin Binding Site(S) on the Dictyostelium Actin Surface as Identified by Site-Directed Mutagenesis
Authors: Saeki, K. / Sutoh, K. / Wakabayashi, T.
History
DepositionNov 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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
S: GELSOLIN
A: CHIMERIC ACTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6656
Polymers56,0382
Non-polymers6274
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-53 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.893, 69.385, 183.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GELSOLIN


Mass: 14205.001 Da / Num. of mol.: 1 / Fragment: SEGMENT 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Protein CHIMERIC ACTIN


Mass: 41832.715 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum, Tetrahymena thermophila
Genus: Dictyostelium, Tetrahymena / Species: , / Strain: , / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P07830
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, NACL, CACL2, MGCL2, ATP, PEG6000, DTT, NAN3, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMimidazole-HCl1drop
3150 mM1dropNaCl
40.1 mMATP1drop
50.1 mM1dropCaCl2
60.1 mM1dropMgCl2
71 mM1dropNaN3
80.1 mMdithiothreitol1drop
950 mMimidazole-HCl1reservoir
10150 mM1reservoirNaCl
110.1 mMATP1reservoir
120.1 mM1reservoirCaCl2
130.1 mM1reservoirMgCl2
141 mM1reservoirNaN3
1510 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: OTHER / Detector: IMAGE PLATE / Date: Jun 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 96715 / % possible obs: 93.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.055 / % possible all: 88.1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. obs: 27352 / Num. measured all: 96715
Reflection shell
*PLUS
Mean I/σ(I) obs: 19.3

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→10 Å /
RfactorSelection details
Rfree0.214 RANDOM
Rwork0.171 -
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 35 405 4329
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9

+
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