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- PDB-2hu2: CTBP/BARS in ternary complex with NAD(H) and RRTGAPPAL peptide -

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Basic information

Entry
Database: PDB / ID: 2hu2
TitleCTBP/BARS in ternary complex with NAD(H) and RRTGAPPAL peptide
Components
  • 9-mer peptide from Zinc finger protein 217
  • C-terminal-binding protein 1
KeywordsOXIDOREDUCTASE / TRANSCRIPTION CO-REPRESSOR / ZINC FINGER PROTEIN
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 / histone deacetylase complex / white fat cell differentiation / synaptic vesicle endocytosis / GABA-ergic synapse / transcription repressor complex / transcription corepressor binding / transcription coregulator binding / PDZ domain binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / NAD binding / presynapse / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / membrane fusion / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / neuron projection / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / nucleoplasm / identical protein binding / nucleus / metal ion binding / 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 1 / 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 ...: / 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 1 / 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 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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 / Zinc finger protein 217 / C-terminal binding protein 1 / C-terminal-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsNardini, M. / Bolognesi, M. / Quinlan, K.G.R. / Verger, A. / Francescato, P. / Crossley, M.
CitationJournal: Mol.Cell.Biol. / Year: 2006
Title: Specific Recognition of ZNF217 and Other Zinc Finger Proteins at a Surface Groove of C-Terminal Binding Proteins
Authors: Quinlan, K.G.R. / Nardini, M. / Verger, A. / Francescato, P. / Yaswen, P. / Corda, D. / Bolognesi, M. / Crossley, M.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-terminal-binding protein 1
B: 9-mer peptide from Zinc finger protein 217
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1594
Polymers40,4492
Non-polymers7092
Water34219
1
A: C-terminal-binding protein 1
B: 9-mer peptide from Zinc finger protein 217
hetero molecules

A: C-terminal-binding protein 1
B: 9-mer peptide from Zinc finger protein 217
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3178
Polymers80,8984
Non-polymers1,4194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Unit cell
Length a, b, c (Å)89.310, 89.310, 162.720
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 1 / CtBP1 / C-terminal-binding protein 3 / CtBP3 / 50 kDa BFA-dependent ADP-ribosylation substrate / BARS-50


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) / Gene: Ctbp1, Bars, Ctbp3 / Organ: brain / Plasmid: PET11D-HIS / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)plyss
References: UniProt: Q9Z2F5, UniProt: Q6AZ26*PLUS, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein/peptide 9-mer peptide from Zinc finger protein 217


Mass: 940.101 Da / Num. of mol.: 1 / Fragment: residues 1-9 / Mutation: C5A / Source method: obtained synthetically / Details: This sequence occurs naturally in human (with c5a) / References: UniProt: O75362
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M ammonium formate, 0.1M Hepes (pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.85→55.9 Å / Num. all: 9503 / Num. obs: 9503 / % possible obs: 99.81 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.094 / Net I/σ(I): 21.1
Reflection shellResolution: 2.85→3 Å / Redundancy: 9.52 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.93 / Num. unique all: 1341 / % possible all: 99.99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKU

1hku


Resolution: 2.85→35 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 18.056 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27491 960 10.1 %RANDOM
Rwork0.22685 ---
all0.23172 8533 --
obs0.23172 8533 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.71 Å2
Refinement stepCycle: LAST / Resolution: 2.85→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 44 22 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212717
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.9793682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8395338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05623.226124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02115460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5531527
X-RAY DIFFRACTIONr_chiral_restr0.0630.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022029
X-RAY DIFFRACTIONr_nbd_refined0.1620.21040
X-RAY DIFFRACTIONr_nbtor_refined0.2890.21842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.210
X-RAY DIFFRACTIONr_mcbond_it0.3771.51748
X-RAY DIFFRACTIONr_mcangle_it0.55422701
X-RAY DIFFRACTIONr_scbond_it0.49731036
X-RAY DIFFRACTIONr_scangle_it0.8814.5981
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 80 -
Rwork0.339 593 -
obs--100 %

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