|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 / negative regulation of histone H4 acetylation / presynaptic active zone cytoplasmic component / negative regulation of histone acetylation / 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 / positive regulation of histone deacetylation / GABA-ergic synapse ...Signaling by TCF7L2 mutants / Repression of WNT target genes / negative regulation of histone H4 acetylation / presynaptic active zone cytoplasmic component / negative regulation of histone acetylation / 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 / positive regulation of histone deacetylation / GABA-ergic synapse / viral genome replication / heterochromatin assembly / transcription corepressor binding / transcription repressor complex / SUMOylation of transcription cofactors / 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 / protein C-terminus binding / regulation of cell cycle / negative regulation of cell population proliferation / glutamatergic synapse / protein domain specific binding / negative regulation of transcription, DNA-templated / chromatin binding / protein phosphorylation / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / C-terminal-binding protein 1
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å|
|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.
|Structure viewer||Molecule: |
Downloads & links
A: C-terminal-binding protein 1
A: C-terminal-binding protein 1
A: C-terminal-binding protein 1
|Components on special symmetry positions|
|#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|
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|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
|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|
|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|
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