+Open data
-Basic information
Entry | Database: PDB / ID: 6v89 | ||||||
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Title | Human CtBP1 (28-375) in complex with AMP | ||||||
Components | C-terminal-binding protein 1 | ||||||
Keywords | TRANSCRIPTION / co-transcriptional factor | ||||||
Function / homology | Function and homology information Signaling by TCF7L2 mutants / Repression of WNT target genes / 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 / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex ...Signaling by TCF7L2 mutants / Repression of WNT target genes / 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 / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / viral genome replication / transcription corepressor binding / SUMOylation of transcription cofactors / transcription coregulator binding / Deactivation of the beta-catenin transactivating complex / transcription corepressor activity / NAD binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / 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 / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Royer, W.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: NAD(H) phosphates mediate tetramer assembly of human C-terminal binding protein (CtBP). Authors: Nichols, J.C. / Schiffer, C.A. / Royer Jr., W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v89.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v89.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 6v89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v89_validation.pdf.gz | 327 KB | Display | wwPDB validaton report |
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Full document | 6v89_full_validation.pdf.gz | 327 KB | Display | |
Data in XML | 6v89_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 6v89_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v89 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v89 | HTTPS FTP |
-Related structure data
Related structure data | 6v8aC 7kwmC 6cdfS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40537.094 Da / Num. of mol.: 1 / Fragment: UNP residues 28-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP1, CTBP / Production host: Escherichia coli (E. coli) References: UniProt: Q13363, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor | ||||||
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#2: Chemical | ChemComp-AMP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 80-200 mM calcium chloride, 2-6% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 22, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. obs: 13982 / % possible obs: 94.4 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Χ2: 1.029 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6CDF Resolution: 2.45→36.14 Å / SU ML: 0.3851 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0665
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→36.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 3.05071588489 Å / Origin y: 32.2686866215 Å / Origin z: -26.4542509842 Å
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Refinement TLS group | Selection details: all |