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Yorodumi- PDB-6c9m: The Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c9m | ||||||
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Title | The Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex | ||||||
Components |
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Keywords | TRANSFERASE / NatA / N-terminal acetylation / protein complex | ||||||
Function / homology | Function and homology information negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-acetyltransferase activity / internal protein amino acid acetylation / protein acetylation ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-acetyltransferase activity / internal protein amino acid acetylation / protein acetylation / chromosome organization / ribosome binding / angiogenesis / transcription regulator complex / cell differentiation / nuclear body / protein stabilization / intracellular membrane-bounded organelle / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / RNA binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Gottlieb, L. / Marmorstein, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2018 Title: Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Authors: Gottlieb, L. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c9m.cif.gz | 771 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c9m.ent.gz | 642 KB | Display | PDB format |
PDBx/mmJSON format | 6c9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9m ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9m | HTTPS FTP |
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-Related structure data
Related structure data | 6c95C 4kvoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 101427.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA15, GA19, NARG1, NATH, TBDN100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXJ9 #2: Protein | Mass: 26522.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA10, ARD1, ARD1A, TE2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA #3: Chemical | #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | |
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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: 2.85 Å3/Da / Density % sol: 56.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350, 10% Tascimate, pH 7.5, 2% acetone |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2017 |
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.95 Å / Num. obs: 72780 / % possible obs: 99.8 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 1.44 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4KVO Resolution: 2.8→48.95 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.6 / Phase error: 26.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.95 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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