+Open data
-Basic information
Entry | Database: PDB / ID: 3phd | ||||||
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Title | Crystal structure of human HDAC6 in complex with ubiquitin | ||||||
Components |
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Keywords | PROTEIN BINDING / HDAC6 / ubiquitin / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / negative regulation of protein-containing complex disassembly / protein-containing complex disassembly / negative regulation of axon extension involved in axon guidance / tubulin deacetylation / regulation of establishment of protein localization / : / : / positive regulation of tubulin deacetylation / Cilium Assembly / regulation of autophagy of mitochondrion / peptidyl-lysine deacetylation / collateral sprouting / protein modification process => GO:0036211 / tubulin deacetylase activity / Transcriptional regulation by RUNX2 / lysosome localization / negative regulation of microtubule depolymerization / negative regulation of protein acetylation / misfolded protein binding / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein deacetylation / cilium disassembly / response to growth factor / dendritic spine morphogenesis / aggresome assembly / histone deacetylase / regulation of androgen receptor signaling pathway / cellular response to misfolded protein / protein lysine deacetylase activity / hypothalamus gonadotrophin-releasing hormone neuron development / positive regulation of signaling receptor activity / aggresome / cellular response to parathyroid hormone stimulus / female meiosis I / positive regulation of dendrite morphogenesis / positive regulation of protein monoubiquitination / microtubule associated complex / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitochondrion transport along microtubule / regulation of fat cell differentiation / histone deacetylase activity / fat pad development / negative regulation of gene expression, epigenetic / dynein complex binding / response to corticosterone / protein quality control for misfolded or incompletely synthesized proteins / beta-tubulin binding / axonal transport of mitochondrion / female gonad development / response to dexamethasone / positive regulation of epithelial cell migration / seminiferous tubule development / Notch-HLH transcription pathway / male meiosis I / cell leading edge / RUNX2 regulates osteoblast differentiation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / histone deacetylase complex / Response of EIF2AK4 (GCN2) to amino acid deficiency / alpha-tubulin binding / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / polyubiquitin modification-dependent protein binding / cilium assembly / response to immobilization stress / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / HSF1 activation / regulation of macroautophagy / negative regulation of protein-containing complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / inclusion body / axon cytoplasm / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Dong, A. / Qui, W. / Ravichandran, M. / Schuetz, A. / Loppnau, P. / Li, F. / Mackenzie, F. / Kozieradzki, I. / Ouyang, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Protein Aggregates Are Recruited to Aggresome by Histone Deacetylase 6 via Unanchored Ubiquitin C Termini. Authors: Ouyang, H. / Ali, Y.O. / Ravichandran, M. / Dong, A. / Qiu, W. / Mackenzie, F. / Dhe-Paganon, S. / Arrowsmith, C.H. / Zhai, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3phd.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3phd.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 3phd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/3phd ftp://data.pdbj.org/pub/pdb/validation_reports/ph/3phd | HTTPS FTP |
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-Related structure data
Related structure data | 3c5kS 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: 12023.739 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6, KIAA0901, JM21 / Plasmid: PET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA-R3 / References: UniProt: Q9UBN7, histone deacetylase #2: Protein | Mass: 8576.831 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB, UBA52, UBCEP2, UBC, RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG47*PLUS #3: Chemical | ChemComp-ZN / #4: 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: 3.22 Å3/Da / Density % sol: 61.84 % |
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Crystal grow | Temperature: 297 K / pH: 5.6 Details: 15% PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, temperature 297K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 22204 / Num. obs: 22204 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Biso Wilson estimate: 92.68 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 45.8 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3C5K Resolution: 3→32.72 Å / Cor.coef. Fo:Fc: 0.9073 / Cor.coef. Fo:Fc free: 0.8561 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 72.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.422 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→32.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.15 Å / Total num. of bins used: 11
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