+Open data
-Basic information
Entry | Database: PDB / ID: 6v8a | ||||||
---|---|---|---|---|---|---|---|
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: 2.35 Å | ||||||
Authors | Royer, W.E. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6v8a.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6v8a.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 6v8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v8a_validation.pdf.gz | 328 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6v8a_full_validation.pdf.gz | 328 KB | Display | |
Data in XML | 6v8a_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 6v8a_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8a ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8a | HTTPS FTP |
-Related structure data
Related structure data | 6v89C 7kwmC 6cdfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 40539.066 Da / Num. of mol.: 1 / Fragment: UNP residues 28-375 / Mutation: V185T 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 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-AMP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.05 % |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 3, 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: 2.35→50 Å / Num. obs: 16758 / % possible obs: 99.7 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.107 / Χ2: 0.939 / Net I/σ(I): 6.4 / Num. measured all: 157772 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDb entry 6CDF Resolution: 2.35→31.55 Å / SU ML: 0.2759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4615
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→31.55 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 2.74466670686 Å / Origin y: 32.5396989643 Å / Origin z: -26.5986527754 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |