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- PDB-1hku: CtBP/BARS: a dual-function protein involved in transcription core... -

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Basic information

Entry
Database: PDB / ID: 1hku
TitleCtBP/BARS: a dual-function protein involved in transcription corepression and Golgi membrane fission
ComponentsC-TERMINAL BINDING PROTEIN 3
KeywordsTRANSCRIPTION / TRANSCRIPTION CO-REPRESSOR / TRANSCRIPTION CO-REPRESSION / ACYLTRANSFERASE / BREFELDIN A / NAD / GOLGI MEMBRANE / ACYL-COA
Function / homology
Function and homology information


presynapse to nucleus signaling pathway / SUMOylation of transcription cofactors / Repression of WNT target genes / 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 ...presynapse to nucleus signaling pathway / SUMOylation of transcription cofactors / Repression of WNT target genes / 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 / lncRNA binding / white fat cell differentiation / synaptic vesicle endocytosis / Notch signaling pathway / transcription repressor complex / transcription corepressor binding / transcription coregulator binding / PDZ domain binding / GABA-ergic synapse / NAD binding / transcription corepressor activity / 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 / chromatin binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / identical protein binding / nucleus / cytoplasm
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 ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / C-terminal-binding protein 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsNardini, 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
DepositionMar 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-TERMINAL BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3735
Polymers39,5251
Non-polymers8484
Water2,054114
1
A: C-TERMINAL BINDING PROTEIN 3
hetero molecules

A: C-TERMINAL BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,74510
Polymers79,0502
Non-polymers1,6958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)88.705, 88.705, 163.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein C-TERMINAL BINDING PROTEIN 3 / CTBP3


Mass: 39525.133 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
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSSIBLLY NVOLVED IN CONTROLLING THE EQUILIBRIUM BETWEEN TUBULAR AND STACKED STRUCTURES IN THE GOLGI COMPLEX.
Has protein modificationY
Sequence detailsHIS-TAG (MGHHHHHH), TRUNCATION AFTER RESIDUE 350

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growpH: 7.5 / Details: 2.0 M AMMONIUM FORMATE, 100 MM HEPES, PH 7.5.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.8-2.1 Mammonium formate1reservoir
2100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 17070 / % possible obs: 99.3 % / Redundancy: 11 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 25.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 8.7 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Redundancy: 11 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 8.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→40 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 INTENTIONALLY CONVERTED TO ATOM N OF THR A347 IN ORDER TO COMPLY WITH ...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 INTENTIONALLY CONVERTED TO ATOM N OF THR A347 IN ORDER TO COMPLY WITH THE PDB FORMAT. THIS CHANGE MAKES NO DECISION ON THE DIRECTION IN WHICH THE CHAIN BRANCHES.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1652 10 %RANDOM
Rwork0.222 ---
obs0.222 16567 94.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 56 114 2732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.6

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