[English] 日本語
Yorodumi
- PDB-1c0f: CRYSTAL STRUCTURE OF DICTYOSTELIUM CAATP-ACTIN IN COMPLEX WITH GE... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1c0f
TitleCRYSTAL STRUCTURE OF DICTYOSTELIUM CAATP-ACTIN IN COMPLEX WITH GELSOLIN SEGMENT 1
Components
  • ACTIN
  • GELSOLIN SEGMENT 1
KeywordsCONTRACTILE PROTEIN / CA ACTIN
Function / homologyActin/actin-like conserved site / Villin/Gelsolin / Actin, conserved site / ADF-H/Gelsolin-like domain superfamily / Gelsolin / Actin / Gelsolin repeat / Actins signature 1. / Actins signature 2. / Actins and actin-related proteins signature. ...Actin/actin-like conserved site / Villin/Gelsolin / Actin, conserved site / ADF-H/Gelsolin-like domain superfamily / Gelsolin / Actin / Gelsolin repeat / Actins signature 1. / Actins signature 2. / Actins and actin-related proteins signature. / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Caspase-mediated cleavage of cytoskeletal proteins / Neutrophil degranulation / Actin family / Amyloid fiber formation / Gelsolin-like domain / intranuclear rod / phototaxis / cell pole / phagolysosome / regulation of establishment of T cell polarity / positive regulation of keratinocyte apoptotic process / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / striated muscle atrophy / positive regulation of protein processing in phagocytic vesicle / actin cap / positive regulation of actin nucleation / sequestering of actin monomers / regulation of podosome assembly / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / myosin II binding / sarcoplasm / negative regulation of viral entry into host cell / actin filament severing / barbed-end actin filament capping / actin nucleation / tissue regeneration / phagocytic cup / hyperosmotic response / oligodendrocyte development / early phagosome / actin filament capping / cortical actin cytoskeleton / response to folic acid / myosin binding / podosome / lipid droplet / pseudopodium / cell leading edge / hepatocyte apoptotic process / cilium assembly / regulation of cell adhesion / mitotic cytokinesis / phagocytic vesicle / phagocytosis / amyloid fibril formation / actin filament reorganization / actin filament polymerization / vesicle-mediated transport / response to cAMP / endocytic vesicle / phosphatidylinositol-mediated signaling / actin filament / cellular response to interferon-gamma / structural constituent of cytoskeleton / ruffle / protein destabilization / cell morphogenesis / phagocytosis, engulfment / cellular response to cadmium ion / actin cytoskeleton / cell cortex / endocytosis / actin filament binding / lamellipodium / actin binding / chemotaxis / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / blood microparticle / aging / myelin sheath / focal adhesion / cellular protein metabolic process / positive regulation of gene expression / neutrophil degranulation / calcium ion binding / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol / cytoplasm
Function and homology information
Specimen sourceHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.4 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 16, 1999 / Release: Mar 1, 2000
RevisionDateData content typeGroupProviderType
1.0Mar 1, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: GELSOLIN SEGMENT 1
A: ACTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7906
Polyers55,1632
Non-polymers6274
Water7,224401
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3640
ΔGint (kcal/M)-53
Surface area (Å2)21140
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.000, 69.550, 184.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

-
Components

#1: Protein/peptide GELSOLIN SEGMENT 1


Mass: 14205.001 Da / Num. of mol.: 1 / Mutation: N35C / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Protein/peptide ACTIN /


Mass: 40957.543 Da / Num. of mol.: 1 / Source: (natural) Dictyostelium discoideum (eukaryote) / Genus: Dictyostelium / References: UniProt: P07830
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Formula: Ca / Calcium
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 / Density percent sol: 62.9 %
Crystal growTemp: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: IMIDAZOLE, SODIUM CHLORIDE, ATP, CALCIUM CHLORIDE, MAGNESIUM CHLORIDE, SODIUM AZIDE, DITHIOTHREITOL, PEG 6000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 7
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.6 / Synchrotron site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Apr 5, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionD resolution high: 2.4 Å / D resolution low: 29.1 Å / Number obs: 27962 / Rmerge I obs: 0.074 / NetI over sigmaI: 8 / Percent possible obs: 94.4
Reflection shellRmerge I obs: 0.155 / Highest resolution: 2.4 Å / Lowest resolution: 2.52 Å
Reflection
*PLUS
Number measured all: 68469 / Percent possible obs: 94.9
Reflection shell
*PLUS
MeanI over sigI obs: 4.5

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefineR Free selection details: RANDOM / Cross valid method: THROUGHOUT
Least-squares processR factor R free: 0.231 / R factor R work: 0.183 / Highest resolution: 2.4 Å / Lowest resolution: 1 Å
Refine hist #LASTHighest resolution: 2.4 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 3877 / Nucleic acid: 0 / Ligand: 34 / Solvent: 401 / Total: 4312
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d1.90
X-RAY DIFFRACTIONp_angle_deg1.90
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.010
X-RAY DIFFRACTIONp_angle_d

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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