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Open data
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Basic information
Entry | Database: PDB / ID: 6nas | ||||||
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Title | Ternary Complex of Ac-Alpha-Actin with Profilin and AcCoA-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 / regulation of actin polymerization or depolymerization / synapse maturation / acetyl-CoA binding / peptide alpha-N-acetyltransferase activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity ...N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / actin modification / regulation of actin polymerization or depolymerization / synapse maturation / acetyl-CoA binding / peptide alpha-N-acetyltransferase activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / N-acetyltransferase activity / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / positive regulation of actin filament polymerization / protein acetylation / positive regulation of epithelial cell migration / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / phosphotyrosine residue binding / filopodium / neural tube closure / RHO GTPases Activate Formins / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / modulation of chemical synaptic transmission / small GTPase binding / calcium-dependent protein binding / Platelet degranulation / lamellipodium / actin binding / cell cortex / cell body / actin cytoskeleton organization / cytoskeleton / protein stabilization / blood microparticle / hydrolase activity / cadherin binding / protein domain specific binding / focal adhesion / glutamatergic synapse / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol 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 | ![]() | 274.1 KB | Display | ![]() |
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PDB format | ![]() | 219.4 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 | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nbeC ![]() 6nbwC ![]() 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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1 |
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ANP
#1: Protein | Mass: 41917.668 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, 14 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/LAB.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACO.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/ACO.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-ACO / | #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: 2.33 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16% Peg3350, 0.1 MES pH 6.5, 0.2M 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: 2.899→50 Å / Num. obs: 17781 / % possible obs: 100 % / Redundancy: 39.4 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 40.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 1744 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PBD Resolution: 2.9→28.72 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.79 / 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: 149.88 Å2 / Biso mean: 44.1477 Å2 / Biso min: 17.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→28.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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