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Yorodumi- PDB-3q35: Structure of the Rtt109-AcCoA/Vps75 complex and implications for ... -
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-Basic information
Entry | Database: PDB / ID: 3q35 | ||||||
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Title | Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation | ||||||
Components |
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Keywords | TRANSFERASE/CHAPERONE / Rtt109:Vps75=2:2 stoichiometry complex / Acetyl Coenzyme A (ACoA) bound / autoacetylation at Rtt109 Lys290 / nuclear / TRANSFERASE-CHAPERONE complex | ||||||
Function / homology | Function and homology information : / : / : / : / histone H3K23 acetyltransferase activity / : / histone H3K56 acetyltransferase activity / : / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly ...: / : / : / : / histone H3K23 acetyltransferase activity / : / histone H3K56 acetyltransferase activity / : / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / : / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / acetyltransferase activator activity / peptidyl-lysine acetylation / replication-born double-strand break repair via sister chromatid exchange / histone H3 acetyltransferase activity / retrotransposon silencing / : / histone H3K27 acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / protein acetylation / histone acetyltransferase / nucleosome assembly / double-strand break repair via nonhomologous end joining / protein transport / histone binding / regulation of gene expression / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Tang, Y. / Yuan, H. / Meeth, K. / Marmorstein, R. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation. Authors: Tang, Y. / Holbert, M.A. / Delgoshaie, N. / Wurtele, H. / Guillemette, B. / Meeth, K. / Yuan, H. / Drogaris, P. / Lee, E.H. / Durette, C. / Thibault, P. / Verreault, A. / Cole, P.A. / Marmorstein, R. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. Authors: Tang, Y. / Holbert, M.A. / Wurtele, H. / Meeth, K. / Rocha, W. / Gharib, M. / Jiang, E. / Thibault, P. / Verreault, A. / Verrault, A. / Cole, P.A. / Marmorstein, R. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Structure of Vps75 and implications for histone chaperone function. Authors: Tang, Y. / Meeth, K. / Jiang, E. / Luo, C. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q35.cif.gz | 270.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q35.ent.gz | 217.9 KB | Display | PDB format |
PDBx/mmJSON format | 3q35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/3q35 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/3q35 | HTTPS FTP |
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-Related structure data
Related structure data | 3q33SC 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
#1: Protein | Mass: 50348.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: BamHI/XhoI insert Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: KIM2, L1377, REM50, RTT109, YLL002W / Plasmid: 6His-TEV-pCDF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q07794, histone acetyltransferase |
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#2: Protein | Mass: 27292.619 Da / Num. of mol.: 1 / Fragment: unp residues 1-232 Source method: isolated from a genetically manipulated source Details: BamHI/XhoI insert Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: N0890, VPS75, YNL246W / Plasmid: GST-TEV-pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: P53853 |
#3: Chemical | ChemComp-ACO / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10.0% (v/v) PEG8000; 8% (v/v) ethylene glycol; 100 mM Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.988 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2008 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 15348 / Num. obs: 15302 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.083 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.427 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3Q33 Resolution: 3.3→48.01 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.394 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.3→48.01 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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