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- PDB-6nbw: Ternary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nbw | ||||||
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Title | Ternary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80 | ||||||
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![]() | STRUCTURAL PROTEIN/TRANSFERASE / acetylation / NAA80 / CYTOSOLIC PROTEIN / STRUCTURAL PROTEIN-TRANSFERASE complex | ||||||
Function / homology | ![]() N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of actin polymerization or depolymerization / synapse maturation / acetyl-CoA binding / peptide alpha-N-acetyltransferase activity / modification of postsynaptic actin cytoskeleton ...N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of actin polymerization or depolymerization / synapse maturation / acetyl-CoA binding / peptide alpha-N-acetyltransferase activity / modification of postsynaptic actin cytoskeleton / regulation of transepithelial transport / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / Gap junction degradation / Signaling by ROBO receptors / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of actin filament polymerization / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / N-acetyltransferase activity / tight junction / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / regulation of norepinephrine uptake / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of ruffle assembly / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / negative regulation of stress fiber assembly / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of actin filament polymerization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / protein acetylation / nitric-oxide synthase binding / positive regulation of epithelial cell migration / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / actin monomer binding / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / EPHB-mediated forward signaling / substantia nigra development / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / axonogenesis / negative regulation of protein binding / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / regulation of transmembrane transporter activity / adherens junction / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rebowski, G. / Boczkowska, M. / Dominguez, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of actin N-terminal acetylation. Authors: Rebowski, G. / Boczkowska, M. / Drazic, A. / Ree, R. / Goris, M. / Arnesen, T. / Dominguez, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.7 KB | Display | ![]() |
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PDB format | ![]() | 218 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nasC ![]() 6nbeC ![]() 2pbdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ANP
#1: Protein | Mass: 41664.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 25923.076 Da / Num. of mol.: 1 / Fragment: residues 56-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q93015, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
#3: Protein | Mass: 15071.222 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 7 types, 211 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/LAB.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SOP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/LAB.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SOP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / | ||||||
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#5: Chemical | ChemComp-ATP / | ||||||
#6: Chemical | ChemComp-LAB / | ||||||
#7: Chemical | #8: Chemical | ChemComp-SOP / [( | #9: Chemical | ChemComp-MES / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% PEG 3350, 50mM MES pH6.2, 50mM NH4NO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 |
Reflection | Resolution: 2.496→50 Å / Num. obs: 28132 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 4 / Num. unique obs: 2785 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PBD Resolution: 2.5→26.1 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.16 Å2 / Biso mean: 43.413 Å2 / Biso min: 24.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→26.1 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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