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- PDB-1yvn: THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SE... -

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Entry
Database: PDB / ID: 1yvn
TitleTHE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SEGMENT 1.
Components
  • PROTEIN (ACTIN)
  • PROTEIN (GELSOLIN)
KeywordsSTRUCTURAL PROTEIN / YEAST / ACTIN / MUTANT V159N / GELSOLIN / ACTIN-BINDING / MG-ATP
Function / homologyActin / RHO GTPases Activate WASPs and WAVEs / Actins and actin-related proteins signature. / Actins signature 2. / Caspase-mediated cleavage of cytoskeletal proteins / Actins signature 1. / Neutrophil degranulation / Amyloid fiber formation / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases activate IQGAPs ...Actin / RHO GTPases Activate WASPs and WAVEs / Actins and actin-related proteins signature. / Actins signature 2. / Caspase-mediated cleavage of cytoskeletal proteins / Actins signature 1. / Neutrophil degranulation / Amyloid fiber formation / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases activate IQGAPs / Neutrophil degranulation / Actin family / Actin, conserved site / Villin/Gelsolin / Gelsolin-like domain / Actin/actin-like conserved site / ADF-H/Gelsolin-like domain superfamily / Gelsolin / Gelsolin repeat / budding cell isotropic bud growth / cellular bud neck contractile ring / actomyosin contractile ring contraction / mitochondrion inheritance / ascospore wall assembly / vesicle transport along actin filament / vacuole inheritance / positive regulation of keratinocyte apoptotic process / renal protein absorption / regulation of establishment of T cell polarity / striated muscle atrophy / regulation of plasma membrane raft polarization / regulation of receptor clustering / positive regulation of protein processing in phagocytic vesicle / actin cap / Swr1 complex / chronological cell aging / 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 / fungal-type cell wall organization / myosin II binding / Ino80 complex / actin cortical patch / sarcoplasm / negative regulation of viral entry into host cell / actin filament severing / barbed-end actin filament capping / actin nucleation / tissue regeneration / NuA4 histone acetyltransferase complex / oligodendrocyte development / actin filament capping / cortical actin cytoskeleton / establishment of mitotic spindle orientation / response to folic acid / podosome / actin filament bundle / cilium assembly / hepatocyte apoptotic process / exocytosis / protein secretion / regulation of cell adhesion / histone acetylation / phagocytic vesicle / amyloid fibril formation / actin filament reorganization / actin filament polymerization / establishment of cell polarity / actin filament / cellular response to interferon-gamma / structural constituent of cytoskeleton / phosphatidylinositol-mediated signaling / ruffle / protein destabilization / phagocytosis, engulfment / cellular response to cadmium ion / actin cytoskeleton / cellular response to oxidative stress / endocytosis / lamellipodium / actin filament binding / actin binding / myelin sheath / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / blood microparticle / aging / DNA repair / 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
Function and homology information
Specimen sourceHomo sapiens (human)
Saccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.1 Å resolution
AuthorsVorobiev, S.M. / Belmont, L.D. / Drubin, D.G. / Almo, S.C.
Citation
Journal: To be Published
Title: Crystal structure of yeast actin V159N mutant
Authors: Vorobiev, S.M. / Belmont, L.D. / Drubin, D.D. / Almos, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: A Change in Actin Conformation Associated with Filament Instability After Pi Release
Authors: Belmont, L.D. / Orlova, A. / Drubin, D.G. / Egelman, E.H.
#2: 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.
#3: Journal: Nature / Year: 1990
Title: Atomic Structure of the Actin:DNase I Complex
Authors: Kabash, W. / Mannhertz, H.G. / Suck, D. / Pai, E.F. / Holmes, K.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 23, 1999 / Release: Mar 23, 2000
RevisionDateData content typeGroupProviderType
1.0Mar 23, 2000Structure modelrepositoryInitial release
1.1Apr 26, 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
A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4906
Polyers55,8222
Non-polymers6684
Water5,098283
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3400
ΔGint (kcal/M)-49
Surface area (Å2)20920
MethodPISA
2
A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules

A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,98012
Polyers111,6454
Non-polymers1,3358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)9230
ΔGint (kcal/M)-133
Surface area (Å2)39410
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)176.098, 68.077, 54.691
Angle α, β, γ (deg.)90.00, 102.24, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

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Protein/peptide , 2 types, 2 molecules AG

#1: Protein/peptide PROTEIN (ACTIN)


Mass: 41750.520 Da / Num. of mol.: 1 / Details: MG-ATP BOUND ACTIN / Mutation: V159N / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Details: THE GENE NAME IS ACT. / Genus: Saccharomyces / Strain: ACT1-159 / References: UniProt: P60010
#2: Protein/peptide PROTEIN (GELSOLIN)


Mass: 14071.831 Da / Num. of mol.: 1 / Details: CA(2+)-BOUND PROTEIN / Fragment: FRAGMENT 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Description: SYNTHETIC GENEArtificial gene synthesis / Plasmid name: PMW172 / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06396

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Non-polymers , 5 types, 287 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.51 / Density percent sol: 50.55 %
Crystal growpH: 8
Details: 0.1 M HEPES, 1.60 M (NH4)2SO4, 2 MM MG-ATP, PH=8.0.

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Data collection

DiffractionMean temperature: 105 kelvins
SourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0702
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Feb 1, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0702 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 25 Å / Number obs: 33130 / Rmerge I obs: 0.057 / Redundancy: 2.95 % / Percent possible obs: 86.8

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YAG
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 22.69 Å2
Least-squares processR factor R free: 0.235 / R factor R work: 0.187 / Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Number reflection obs: 32577 / Percent reflection R free: 4 / Percent reflection obs: 84.4
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 25 Å
Number of atoms included #LASTProtein: 3869 / Nucleic acid: 0 / Ligand: 38 / Solvent: 283 / Total: 4190
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.404
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.35
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.736
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS shellHighest resolution: 2.1 Å / R factor R free: 0.275 / R factor R work: 0.229 / Lowest resolution: 2.2 Å / Total number of bins used: 8 / Percent reflection R free: 3.5 / Percent reflection obs: 62.82
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH19.SOL
X-RAY DIFFRACTION3PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION4PARAM.ATPTOPOLOGY.ATP

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