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Yorodumi- PDB-1yvn: THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yvn | ||||||
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Title | THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SEGMENT 1. | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / YEAST / ACTIN / MUTANT V159N / GELSOLIN / ACTIN-BINDING / MG-ATP | ||||||
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: 2.1 Å | ||||||
Authors | Vorobiev, 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: 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 | 1yvn.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yvn.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yvn_validation.pdf.gz | 476.6 KB | Display | wwPDB validaton report |
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Full document | 1yvn_full_validation.pdf.gz | 488.8 KB | Display | |
Data in XML | 1yvn_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1yvn_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yvn ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yvn | HTTPS FTP |
-Related structure data
Related structure data | 1yagS S: Starting model for refinement |
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Similar 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: 41750.520 Da / Num. of mol.: 1 / Mutation: V159N / Source method: isolated from a natural source / Details: THE GENE NAME IS ACT. / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ACT1-159 / References: UniProt: P60010 |
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#2: Protein | Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: FRAGMENT 1 Source method: isolated from a genetically manipulated source Details: CA(2+)-BOUND PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC GENE / Plasmid: PMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06396 |
-Non-polymers , 5 types, 287 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | pH: 8 Details: 0.1 M HEPES, 1.60 M (NH4)2SO4, 2 MM MG-ATP, PH=8.0. |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0702 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0702 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 33130 / % possible obs: 86.8 % / Redundancy: 2.95 % / Rmerge(I) obs: 0.057 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YAG Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 22.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Total num. of bins used: 8
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Xplor file |
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