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- PDB-3q33: Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q33 | ||||||
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Title | Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation | ||||||
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![]() | TRANSFERASE / CHAPERONE/GENE REGULATION / Rtt109:Vps75=2:2 stoichiometry complex / histone acetyltransferase / with Acetyl Coenzyme A (ACoA) bound / autoacetylation on Rtt109 Lys290 / nuclear / TRANSFERASE-CHAPERONE-TRANSCRIPTION REGULATOR complex / TRANSFERASE-CHAPERONE complex / CHAPERONE-GENE REGULATION complex | ||||||
Function / homology | ![]() histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / sexual sporulation resulting in formation of a cellular spore / 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 / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex ...histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / sexual sporulation resulting in formation of a cellular spore / 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 / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / maintenance of rDNA / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange / retrotransposon silencing / histone H3 acetyltransferase activity / replication fork protection complex / histone H3K27 acetyltransferase activity / Oxidative Stress Induced Senescence / peptide-lysine-N-acetyltransferase activity / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / CENP-A containing nucleosome / histone acetyltransferase / protein modification process / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / nucleosome assembly / protein transport / chromatin organization / histone binding / regulation of gene expression / protein heterodimerization activity / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, Y. / Yuan, H. / Meeth, K. / Marmorstein, R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.4 KB | Display | ![]() |
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PDB format | ![]() | 218.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 717.7 KB | Display | ![]() |
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Full document | ![]() | 735.9 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3q35C ![]() 3d35 ![]() 3dm7S 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 , 2 types, 2 molecules AB
#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.) ![]() ![]() Gene: KIM2, L1377, REM50, RTT109, SCY_3578, YLL002W / Plasmid: 6His-TEV-pCDF-Duet / Production host: ![]() ![]() |
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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.) ![]() ![]() Gene: N0890, VPS75, YNL246W / Plasmid: GST-TEV-pRSF-Duet / Production host: ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules D
#3: Protein/peptide | Mass: 1492.727 Da / Num. of mol.: 1 / Fragment: unp residues 1-14 / Source method: obtained synthetically / Source: (synth.) synthetic (others) / References: UniProt: P61830 |
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-Non-polymers , 3 types, 25 molecules ![](data/chem/img/ACO.gif)
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![](data/chem/img/HOH.gif)
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#4: Chemical | ChemComp-ACO / |
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#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 10.0% (v/v) PEG 8000 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: ![]() ![]() ![]() |
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: 2.75→50 Å / Num. obs: 23924 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 80.7 Å2 / Rsym value: 0.047 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.363 / % possible all: 78.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3D35 3DM7 Resolution: 2.8→45.16 Å / Isotropic thermal model: ISOTROPIC / Phase error: 28.43 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso min: 28.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9275 Å /
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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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