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- PDB-1nlv: Crystal Structure Of Dictyostelium Discoideum Actin Complexed Wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nlv | ||||||
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Title | Crystal Structure Of Dictyostelium Discoideum Actin Complexed With Ca ATP And Human Gelsolin Segment 1 | ||||||
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![]() | STRUCTURAL PROTEIN / actin / gelsolin / cytoskeleton / cell motility | ||||||
Function / homology | ![]() 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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cell pole / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / plasma membrane repair / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / early phagosome / hyperosmotic response / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cortical actin cytoskeleton / myosin binding / phagocytosis, engulfment / hepatocyte apoptotic process / cell leading edge / pseudopodium / phagocytic cup / mitotic cytokinesis / endocytic vesicle / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / vesicle-mediated transport / phagocytic vesicle / response to cAMP / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / lipid droplet / 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 / cell morphogenesis / structural constituent of cytoskeleton / cellular response to type II interferon / endocytosis / chemotaxis / actin filament binding / cell-cell junction / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S.M. / Welti, S. / Condeelis, J. / Almo, S.C. | ||||||
![]() | ![]() Title: The Structure of Non-Vertebrate Actin: Implications For The ATP Hydrolytic Mechanism Authors: Vorobiev, S.M. / Strokopytov, B. / Drubin, D.G. / Frieden, C. / Ono, S. / Condeelis, J. / Rubenstein, P.A. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.9 KB | Display | ![]() |
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PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1d4xC ![]() 1nm1C ![]() 1nmdC ![]() 1yagC ![]() 1dagS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 41647.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: DOMAIN 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 337 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/SO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/SO2.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ATP / | #6: Chemical | ChemComp-SO2 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: lithium chloride, magnesium chloride, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07018 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→23 Å / Num. all: 61207 / Num. obs: 61207 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.14 % |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.338 / Num. unique all: 6067 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DAG Resolution: 1.8→23 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→23 Å
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