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- PDB-1yag: STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX -

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Entry
Database: PDB / ID: 1yag
TitleSTRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX
Components
  • PROTEIN (ACTIN)
  • PROTEIN (GELSOLIN)
KeywordsCONTRACTILE PROTEIN / COMPLEX / ACTIN / GELSOLIN
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 / 1.9 Å resolution
AuthorsVorobiev, S. / Strokopytov, B. / Frieden, C. / Almo, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The structure of nonvertebrate actin: Implications for the ATP hydrolytic mechanism
Authors: Vorobiev, S. / Strokopytov, B. / Drubin, D.G. / Frieden, C. / Ono, S. / Condeelis, J. / Rubenstein, P.A. / Almo, S.C.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: The Structure of an Open State of Beta-Actin at 2.65 A Resolution
Authors: Chik, J.K. / Lindberg, U. / Schutt, C.E.
#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: Kabsch, W. / Mannherz, H.G. / Suck, D. / Pai, E.F. / Holmes, K.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 9, 1998 / Release: Oct 9, 1999
RevisionDateData content typeGroupProviderType
1.0Oct 9, 1999Structure modelrepositoryInitial release
1.1Oct 16, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,4756
Polyers55,8072
Non-polymers6684
Water7,692427
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3240
ΔGint (kcal/M)-38
Surface area (Å2)21100
MethodPISA,PQS
2
A: PROTEIN (ACTIN)
G: PROTEIN (GELSOLIN)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)112,95012
Polyers111,6154
Non-polymers1,3358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area (Å2)9290
ΔGint (kcal/M)-130
Surface area (Å2)39760
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)176.662, 68.099, 54.598
Angle α, β, γ (deg.)90.00, 102.55, 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: 41735.547 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Genus: Saccharomyces / Strain: RED STAR / References: UniProt: P60010
#2: Protein/peptide PROTEIN (GELSOLIN) / ACTIN-DEPOLYMERIZING FACTOR (ADF)


Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: SUBDOMAIN 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / 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, 431 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.: 427 / Formula: H2O / Water

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Details

Nonpolymer detailsAN ORDERED MAGNESIUM ION IS OBSERVED BOUND TO ATP.

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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: 2.87 / Density percent sol: 50.5 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
11.4-1.7 Mammonium sulfatereservoir
2100 mMHEPESreservoir
32 mMMg-ATPreservoir
52 mMTris-HCldrop
62 mMATPdrop
74 mMdropMgCl2
80.5 mMEGTAdrop
91 mMdropNaN3
4gelositindrop1:1.25 stoichiometry

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Data collection

DiffractionMean temperature: 93 kelvins
SourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Jun 15, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionD resolution high: 1.9 Å / D resolution low: 2 Å / Number obs: 49913 / Observed criterion sigma I: 0 / Rmerge I obs: 0.081 / Redundancy: 3.8 % / Percent possible obs: 1
Reflection shellRmerge I obs: 0.36 / Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å / Redundancy: 3.5 % / Percent possible all: 99
Reflection
*PLUS
Redundancy: 3.77 %
Reflection shell
*PLUS
Percent possible obs: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RABBIT SKELETAL MUSCLE ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX

R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 23.71 Å2
Least-squares processR factor R free: 0.231 / R factor R work: 0.193 / R factor obs: 0.193 / Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Number reflection obs: 49883 / Percent reflection R free: 5 / Percent reflection obs: 1
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 3883 / Nucleic acid: 0 / Ligand: 38 / Solvent: 427 / Total: 4348
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.89
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
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.2304 / R factor R work: 0.1915 / R factor obs: 0.1915
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.532
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.89

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