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- PDB-1hl3: CtBP/BARS in ternary complex with NAD(H) and PIDLSKK peptide -

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Basic information

Entry
Database: PDB / ID: 1hl3
TitleCtBP/BARS in ternary complex with NAD(H) and PIDLSKK peptide
Components
  • C-TERMINAL BINDING PROTEIN 3
  • PRO-ILE-ASP-LEU-SER-LYS-LYS PEPTIDE
KeywordsTRANCRIPTION CO-REPRESSOR / TRANSCRIPTION CO-REPRESSION / ACYLTRANSFERASE / BREFELDIN A / NAD / GOLGI MEMBRANE / ACYL-COA
Function / homology
Function and homology information


SUMOylation of transcription cofactors / Repression of WNT target genes / presynapse to nucleus signaling pathway / 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 ...SUMOylation of transcription cofactors / Repression of WNT target genes / presynapse to nucleus signaling pathway / 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 / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / transcription corepressor binding / PDZ domain binding / transcription coregulator binding / transcription corepressor activity / NAD binding / presynapse / 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 / glutamatergic synapse / chromatin binding / regulation of transcription by RNA polymerase II / 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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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 ...C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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, 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / C-terminal-binding protein 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 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 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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
B: PRO-ILE-ASP-LEU-SER-LYS-LYS PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9753
Polymers40,3112
Non-polymers6631
Water64936
1
A: C-TERMINAL BINDING PROTEIN 3
B: PRO-ILE-ASP-LEU-SER-LYS-LYS PEPTIDE
hetero molecules

A: C-TERMINAL BINDING PROTEIN 3
B: PRO-ILE-ASP-LEU-SER-LYS-LYS PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9496
Polymers80,6224
Non-polymers1,3272
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)84.811, 84.811, 159.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsCHAIN A FORMS A DIMERIC COMPLEX, BUT SINCE IT IS INCOMPLEX WITH PEPTIDE CHAIN B, THESE RECORDS INDICATEA TETRAMER.

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Components

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


Mass: 39509.133 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: Protein/peptide PRO-ILE-ASP-LEU-SER-LYS-LYS PEPTIDE


Mass: 801.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSSIBLLY NVOLVED IN CONTROLLING THE EQUILIBRIUM BETWEEN TUBULAR AND STACKED STRUCTURES IN THE ...POSSIBLLY NVOLVED IN CONTROLLING THE EQUILIBRIUM BETWEEN TUBULAR AND STACKED STRUCTURES IN THE GOLGI COMPLEX. PIDLSKK (B1-7) PEPTIDE BOUND TO CTBP/BARS
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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growpH: 7.5
Details: 2.0 M AMMONIUM FORMATE, 100 MM HEPES, PH 7.5.CRYSTAL SOAKED IN 5MM PEPTIDE (PIDLSKK)
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: ID14-2 / Wavelength: 0.933
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 6482 / % possible obs: 97.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.9
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.5 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 30 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.125
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1HKU

1hku


Resolution: 3.1→30 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 CHANGED TO ATOM N OF THR A346 IN ORDER TO COMPLY WITH THE PDB FORMAT. ...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 CHANGED TO ATOM N OF THR A346 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
Rfree0.315 668 10 %RANDOM
Rwork0.256 ---
obs0.256 6060 90.8 %-
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 44 36 2697
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.2
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
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.1

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