+Open data
-Basic information
Entry | Database: PDB / ID: 7kwm | ||||||
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Title | CtBP1 (28-375) L182F/V185T - AMP | ||||||
Components | C-terminal-binding protein 1 | ||||||
Keywords | TRANSCRIPTION / C-terminal Binding Protein / Co-transcriptional factor / D-isomer specific 2-hydroxyacid dehydrogenase | ||||||
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 / SUMOylation of transcription cofactors / transcription corepressor binding / Deactivation of the beta-catenin transactivating complex / transcription coregulator binding / 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: 2.3 Å | ||||||
Authors | Royer, W.E. / Del Campo, M. | ||||||
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 | 7kwm.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kwm.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 7kwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/7kwm ftp://data.pdbj.org/pub/pdb/validation_reports/kw/7kwm | HTTPS FTP |
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-Related structure data
Related structure data | 6v89SC 6v8aC 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: 38541.844 Da / Num. of mol.: 1 / Fragment: UNP residues 28-356 / Mutation: L182F, V185T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP1, CTBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q13363 |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 140 mM calcium chloride, 4% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 10, 2020 / Details: VariMax HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30.16 Å / Num. obs: 17800 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.86 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.65 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 1723 / CC1/2: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6V89 Resolution: 2.3→30.16 Å / SU ML: 0.3069 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3505 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30.16 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: 2.86964836314 Å / Origin y: 32.7417958547 Å / Origin z: -26.3962133346 Å
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Refinement TLS group | Selection details: all |