+Open data
-Basic information
Entry | Database: PDB / ID: 3cip | ||||||
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Title | Complex of Dictyostelium Discoideum Actin with Gelsolin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Actin / Gelsolin / Dictyostelium discoideum / Actin-Associated Protein / Methyl Histidine / ATP-binding / Cytoskeleton / Nucleotide-binding / Phosphoprotein / Actin capping / Actin-binding / Alternative initiation / Amyloid / Disease mutation / Secreted | ||||||
Function / homology | Function and homology information intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption ...intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / 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 / cell pole / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / plasma membrane repair / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / early phagosome / cardiac muscle cell contraction / hyperosmotic response / cell projection assembly / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cortical actin cytoskeleton / phagocytosis, engulfment / myosin binding / hepatocyte apoptotic process / cell leading edge / pseudopodium / phagocytic cup / sarcoplasm / mitotic cytokinesis / endocytic vesicle / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / vesicle-mediated transport / response to cAMP / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle / actin filament polymerization / lipid droplet / central nervous system development / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cell morphogenesis / structural constituent of cytoskeleton / cellular response to type II interferon / endocytosis / chemotaxis / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell cortex / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / hydrolase activity / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Baek, K. / Dominguez, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding. Authors: Baek, K. / Liu, X. / Ferron, F. / Shu, S. / Korn, E.D. / Dominguez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cip.cif.gz | 240.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cip.ent.gz | 189.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cip_validation.pdf.gz | 779.6 KB | Display | wwPDB validaton report |
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Full document | 3cip_full_validation.pdf.gz | 782 KB | Display | |
Data in XML | 3cip_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 3cip_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3cip ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3cip | HTTPS FTP |
-Related structure data
Related structure data | 3chwC 3ci5C 1nm1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 41660.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P07830 |
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#2: Protein | Mass: 14338.106 Da / Num. of mol.: 1 / Fragment: Gelsolin Segment 1 (UNP RESIDUES 52-176) Source method: isolated from a genetically manipulated source Details: Intein fusion. Additional Ala-Gly-His at N-terminus after removing fusion tag. Source: (gene. exp.) Homo sapiens (human) / Gene: gsn / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06396 |
-Non-polymers , 6 types, 476 molecules
#3: Chemical | ChemComp-MG / | ||||||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-ATP / | #6: Chemical | #7: Chemical | ChemComp-CA / | #8: 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: 3.03 Å3/Da / Density % sol: 59.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, pH7.5, 1.7M Li2SO4, 2mM ATP, 1mM EDTA, 5% Glycerol, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9999 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2007 / Details: 1-m Pt/Pd-coated ULE mirror |
Radiation | Monochromator: 1-m Pt/Pd-coated ULE mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 88709 / Num. obs: 85829 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.521 / % possible all: 78.4 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NM1 Resolution: 1.6→43.73 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.115 / SU ML: 0.049 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.242 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→43.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.596→1.638 Å / Total num. of bins used: 20
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