+Open data
-Basic information
Entry | Database: PDB / ID: 1yag | ||||||
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Title | STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / COMPLEX / ACTIN / GELSOLIN | ||||||
Function / homology | Function and homology information RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / mitotic actomyosin contractile ring contraction / vacuole inheritance / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / mitotic actomyosin contractile ring contraction / vacuole inheritance / 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 cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / actin cortical patch / negative regulation of viral entry into host cell / Swr1 complex / actin filament severing / actin filament capping / actin filament depolymerization / Ino80 complex / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / establishment of cell polarity / cortical actin cytoskeleton / phagocytosis, engulfment / NuA4 histone acetyltransferase complex / hepatocyte apoptotic process / actin filament bundle / sarcoplasm / protein secretion / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / central nervous system development / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / structural constituent of cytoskeleton / cellular response to type II interferon / actin filament binding / endocytosis / actin cytoskeleton / lamellipodium / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / chromatin remodeling / Amyloid fiber formation / DNA repair / focal adhesion / DNA-templated transcription / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / chromatin / regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Vorobiev, 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yag.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yag.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yag_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 1yag_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 1yag_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1yag_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/1yag ftp://data.pdbj.org/pub/pdb/validation_reports/ya/1yag | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AG
#1: Protein | Mass: 41735.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: RED STAR / References: UniProt: P60010 |
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#2: Protein | Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: SUBDOMAIN 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06396 |
-Non-polymers , 5 types, 431 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-ATP / |
#6: Chemical | ChemComp-CA / |
#7: Water | ChemComp-HOH / |
-Details
Nonpolymer details | AN ORDERED MAGNESIUM ION IS OBSERVED BOUND TO ATP. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 50.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 49913 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / % possible all: 99 |
Reflection | *PLUS Redundancy: 3.77 % |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RABBIT SKELETAL MUSCLE ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 23.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1915 / Rfactor Rfree: 0.2304 / Rfactor Rwork: 0.1915 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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