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Yorodumi- PDB-3tob: Human MOF E350Q crystal structure with active site lysine partial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tob | ||||||
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Title | Human MOF E350Q crystal structure with active site lysine partially acetylated | ||||||
Components | histone acetyltransferase MYST1 | ||||||
Keywords | TRANSFERASE / MYST protein / HAT domain / zinc finger | ||||||
Function / homology | Function and homology information positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / MSL complex / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / MSL complex / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation / post-embryonic hemopoiesis / negative regulation of epithelial to mesenchymal transition / NSL complex / peptide-lysine-N-acetyltransferase activity / oogenesis / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å | ||||||
Authors | Yuan, H. / Ding, E.C. / Marmorstein, R. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: MYST protein acetyltransferase activity requires active site lysine autoacetylation. Authors: Yuan, H. / Rossetto, D. / Mellert, H. / Dang, W. / Srinivasan, M. / Johnson, J. / Hodawadekar, S. / Ding, E.C. / Speicher, K. / Abshiru, N. / Perry, R. / Wu, J. / Yang, C. / Zheng, Y.G. / ...Authors: Yuan, H. / Rossetto, D. / Mellert, H. / Dang, W. / Srinivasan, M. / Johnson, J. / Hodawadekar, S. / Ding, E.C. / Speicher, K. / Abshiru, N. / Perry, R. / Wu, J. / Yang, C. / Zheng, Y.G. / Speicher, D.W. / Thibault, P. / Verreault, A. / Johnson, F.B. / Berger, S.L. / Sternglanz, R. / McMahon, S.B. / Cote, J. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tob.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tob.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tob_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 3tob_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 3tob_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3tob_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/3tob ftp://data.pdbj.org/pub/pdb/validation_reports/to/3tob | HTTPS FTP |
-Related structure data
Related structure data | 3to6C 3to7C 3to9C 3toaC 2givS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 35775.137 Da / Num. of mol.: 1 / Fragment: UNP residues 177-447 / Mutation: E350Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYST1, MOF, PP7073 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7Z6, histone acetyltransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Sequence details | RESIDUE LYS 274 IS PARTIALLY ACETYLATED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG3350, 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 12662 / Num. obs: 12662 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 6.6 / Num. unique all: 614 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GIV Resolution: 2.703→34.522 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 23.73 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.73 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.703→34.522 Å
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Refine LS restraints |
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LS refinement shell |
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