+Open data
-Basic information
Entry | Database: PDB / ID: 1hl3 | ||||||
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Title | CtBP/BARS in ternary complex with NAD(H) and PIDLSKK peptide | ||||||
Components |
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Keywords | TRANCRIPTION 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 / acyltransferase activity ...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 / acyltransferase activity / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / transcription corepressor binding / transcription coregulator binding / PDZ domain binding / transcription corepressor activity / NAD binding / presynapse / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / membrane fusion / transcription coactivator activity / regulation of cell cycle / neuron projection / protein domain specific binding / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / 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) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 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 | 1hl3.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hl3.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 1hl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hl3_validation.pdf.gz | 708.3 KB | Display | wwPDB validaton report |
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Full document | 1hl3_full_validation.pdf.gz | 721.2 KB | Display | |
Data in XML | 1hl3_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1hl3_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/1hl3 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/1hl3 | HTTPS FTP |
-Related structure data
Related structure data | 1hkuSC 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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Details | CHAIN A FORMS A DIMERIC COMPLEX, BUT SINCE IT IS INCOMPLEX WITH PEPTIDE CHAIN B, THESE RECORDS INDICATEA TETRAMER. |
-Components
#1: Protein | Mass: 39509.133 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: Protein/peptide | Mass: 801.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
Compound details | POSSIBLLY NVOLVED IN CONTROLLING THE EQUILIBRIUM BETWEEN TUBULAR AND STACKED STRUCTURES IN THE ...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: 2.17 Å3/Da / Density % sol: 43.3 % | ||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 2.0 M AMMONIUM FORMATE, 100 MM HEPES, PH 7.5.CRYSTAL SOAKED IN 5MM PEPTIDE (PIDLSKK) | ||||||||||||||||||
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: ID14-2 / Wavelength: 0.933 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 6482 / % possible obs: 97.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.5 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 30 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.125 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1HKU Resolution: 3.1→30 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 CHANGED TO ATOM N OF THR A346 IN ORDER TO COMPLY WITH THE PDB FORMAT. ...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 CHANGED TO ATOM N OF THR A346 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: 3.1→30 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.1 |