+Open data
-Basic information
Entry | Database: PDB / ID: 6nbe | ||||||
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Title | Ternary Complex of Ac-Alpha-Actin with Profilin and CoA-NAA80 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/TRANSFERASE / NAA80 / CYTOSOLIC PROTEIN / STRUCTURAL PROTEIN-TRANSFERASE complex | ||||||
Function / homology | Function and homology information N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / actin modification / regulation of actin polymerization or depolymerization / synapse maturation / peptide alpha-N-acetyltransferase activity / acetyl-CoA binding / 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 / peptide alpha-N-acetyltransferase activity / acetyl-CoA binding / 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 / positive regulation of ATP-dependent activity / N-acetyltransferase 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 / tropomyosin binding / myosin heavy chain binding / protein acetylation / positive regulation of epithelial cell migration / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / 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 / cell body / actin binding / cell cortex / actin cytoskeleton organization / blood microparticle / protein stabilization / cytoskeleton / 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 / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Rebowski, G. / Boczkowska, M. / Dominguez, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nbe.cif.gz | 289 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nbe.ent.gz | 231.1 KB | Display | PDB format |
PDBx/mmJSON format | 6nbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/6nbe ftp://data.pdbj.org/pub/pdb/validation_reports/nb/6nbe | HTTPS FTP |
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-Related structure data
Related structure data | 6nasC 6nbwC 2pbdS 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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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) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
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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.) Homo sapiens (human) / Gene: NAA80, FUS2, NAT6 / Production host: Escherichia coli (E. coli) 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.) Homo sapiens (human) / Gene: PFN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07737 |
-Non-polymers , 7 types, 467 molecules
#4: Chemical | ChemComp-CA / | ||||||
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#5: Chemical | ChemComp-ATP / | ||||||
#6: Chemical | ChemComp-LAB / | ||||||
#7: Chemical | #8: Chemical | ChemComp-COA / | #9: Chemical | ChemComp-MES / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.36 % |
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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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å |
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→50 Å / Num. obs: 54090 / % possible obs: 100 % / Redundancy: 26.3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 25.6 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 5172 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PBD Resolution: 2→33.35 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.02 / 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: 121.12 Å2 / Biso mean: 36.62 Å2 / Biso min: 15.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→33.35 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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