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- PDB-1dej: CRYSTAL STRUCTURE OF A DICTYOSTELIUM/TETRAHYMENA CHIMERA ACTIN (M... -

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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 / 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)
Tetrahymena thermophila (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.
#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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: GELSOLIN
A: CHIMERIC ACTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6656
Polyers56,0382
Non-polymers6274
Water7,296405
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3670
ΔGint (kcal/M)-53
Surface area (Å2)21280
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 21

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Components

#1: Protein/peptide GELSOLIN /


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


Mass: 41832.715 Da / Num. of mol.: 1 / Mutation: YES
Source: (gene. exp.) Dictyostelium discoideum, Tetrahymena thermophila
Genus: Dictyostelium, Tetrahymena / Species: , / Strain: , / Genus (production host): Dictyostelium / Production host: Dictyostelium discoideum (eukaryote) / 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.: 405 / Formula: H2O / Water

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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: 3.23 / Density percent sol: 61.87 %
Crystal growTemp: 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
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

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: PHOTON FACTORY BEAMLINE BL-6B / Synchrotron site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: OTHER / Detector: IMAGE PLATE / Collection date: Jun 29, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.4 Å / D resolution low: 3 Å / Number obs: 96715 / Rmerge I obs: 0.033 / NetI over sigmaI: 29.6 / Percent possible obs: 93.5
Reflection shellRmerge I obs: 0.055 / Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Percent possible all: 88.1
Reflection
*PLUS
D resolution high: 2.4 Å / D resolution low: 3 Å / Number obs: 27352 / Number measured all: 96715
Reflection shell
*PLUS
MeanI over sigI obs: 19.3

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineR Free selection details: RANDOM
Least-squares processR factor R free: 0.214 / R factor R work: 0.171 / 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: 3889 / Nucleic acid: 0 / Ligand: 35 / Solvent: 405 / Total: 4329
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.171 / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9

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