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Yorodumi- PDB-1hku: CtBP/BARS: a dual-function protein involved in transcription core... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hku | ||||||
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Title | CtBP/BARS: a dual-function protein involved in transcription corepression and Golgi membrane fission | ||||||
Components | C-TERMINAL BINDING PROTEIN 3 | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION CO-REPRESSOR / TRANSCRIPTION CO-REPRESSION / ACYLTRANSFERASE / BREFELDIN A / NAD / GOLGI MEMBRANE / ACYL-COA | ||||||
Function / homology | Function and homology information SUMOylation of transcription cofactors / Repression of WNT target genes / presynapse to nucleus signaling pathway / Deactivation of the beta-catenin transactivating complex / extrinsic component of presynaptic endocytic zone membrane / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation ...SUMOylation of transcription cofactors / Repression of WNT target genes / presynapse to nucleus signaling pathway / Deactivation of the beta-catenin transactivating complex / extrinsic component of presynaptic endocytic zone membrane / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / acyltransferase activity / synaptic vesicle endocytosis / GABA-ergic synapse / transcription coregulator binding / transcription repressor complex / transcription corepressor binding / PDZ domain binding / transcription corepressor activity / NAD binding / presynapse / DNA-binding transcription factor binding / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / membrane fusion / regulation of cell cycle / neuron projection / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin binding / glutamatergic synapse / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Nardini, M. / Spano, S. / Cericola, C. / Pesce, A. / Massaro, A. / Millo, E. / Luini, A. / Corda, D. / Bolognesi, M. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Ctbp/Bars: A Dual-Function Protein Involved in Transcription Co-Repression and Golgi Membrane Fission Authors: Nardini, M. / Spano, S. / Cericola, C. / Pesce, A. / Massaro, A. / Millo, E. / Luini, A. / Corda, D. / Bolognesi, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Brefeldin A-Adp Ribosylated Substrate (Bars) Authors: Nardini, M. / Spano, S. / Cericola, C. / Pesce, A. / Damonte, G. / Luini, A. / Corda, D. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hku.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hku.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hku_validation.pdf.gz | 773.1 KB | Display | wwPDB validaton report |
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Full document | 1hku_full_validation.pdf.gz | 782.4 KB | Display | |
Data in XML | 1hku_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1hku_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hku ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hku | HTTPS FTP |
-Related 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: 39525.133 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: BRAIN / Plasmid: PET11D-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z2F5 | ||||||
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#2: Chemical | ChemComp-NAD / | ||||||
#3: Chemical | ChemComp-GOL / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | POSSIBLLY NVOLVED IN CONTROLLIN | Sequence details | HIS-TAG (MGHHHHHH), TRUNCATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % | ||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 2.0 M AMMONIUM FORMATE, 100 MM HEPES, PH 7.5. | ||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 17070 / % possible obs: 99.3 % / Redundancy: 11 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 8.7 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Redundancy: 11 % / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 8.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→40 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER Details: NO DENSITY FOR THE HIS-TAG (MGHHHHHH), AND FOR RESIDUES MET A1-HIS A14 AND THR A346-HIS A350. ATOM OXT OF LEU A345 WAS INTENTIONALLY CONVERTED TO ATOM N OF THR A347 IN ORDER TO COMPLY WITH ...Details: NO DENSITY FOR THE HIS-TAG (MGHHHHHH), AND FOR RESIDUES MET A1-HIS A14 AND THR A346-HIS A350. ATOM OXT OF LEU A345 WAS INTENTIONALLY CONVERTED TO ATOM N OF THR A347 IN ORDER TO COMPLY WITH THE PDB FORMAT. THIS CHANGE MAKES NO DECISION ON THE DIRECTION IN WHICH THE CHAIN BRANCHES.
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.6 |