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- PDB-6v8a: Human CtBP1 (28-375) in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 6v8a
TitleHuman CtBP1 (28-375) in complex with AMP
ComponentsC-terminal-binding protein 1
KeywordsTRANSCRIPTION / 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 / lncRNA binding / white fat cell differentiation / synaptic vesicle endocytosis / Notch signaling pathway ...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 / lncRNA binding / white fat cell differentiation / synaptic vesicle endocytosis / Notch signaling pathway / transcription repressor complex / SUMOylation of transcription cofactors / viral genome replication / transcription corepressor binding / transcription coregulator binding / Deactivation of the beta-catenin transactivating complex / GABA-ergic synapse / NAD binding / transcription corepressor activity / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / protein phosphorylation / regulation of cell cycle / protein domain specific binding / negative regulation of cell population proliferation / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRoyer, W.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM119014 United States
CitationJournal: 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
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0336
Polymers40,5391
Non-polymers4945
Water3,963220
1
A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,06512
Polymers81,0782
Non-polymers98710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area8000 Å2
ΔGint-120 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.171, 89.171, 164.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

21A-707-

HOH

31A-716-

HOH

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Components

#1: Protein C-terminal-binding protein 1 / CtBP1


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 / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.35-2.393.20.9857710.766196
2.39-2.434.50.9098100.7661100
2.43-2.485.70.7728350.8231100
2.48-2.536.30.6688100.8471100
2.53-2.596.80.5788010.8671100
2.59-2.657.40.4798230.881100
2.65-2.717.90.4778420.8711100
2.71-2.798.40.3848270.8661100
2.79-2.879.10.3288140.8981100
2.87-2.969.40.2568300.9091100
2.96-3.079.90.2218240.9331100
3.07-3.1910.30.1918340.9471100
3.19-3.3311.60.1428320.9521100
3.33-3.5112.60.1378351.0061100
3.51-3.7312.70.118501.121100
3.73-4.0212.60.0848370.9111100
4.02-4.4212.50.0618630.982199.9
4.42-5.0612.40.0538670.9621100
5.06-6.3712.20.0678940.9731100
6.37-5011.20.0399590.97197.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv1.15refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 6CDF

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
RfactorNum. reflection% reflection
Rfree0.2579 835 5.01 %
Rwork0.2026 --
obs0.2052 16669 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.84 Å2
Refinement stepCycle: LAST / Resolution: 2.35→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 3 220 2725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152575
X-RAY DIFFRACTIONf_angle_d0.45923513
X-RAY DIFFRACTIONf_chiral_restr0.0389418
X-RAY DIFFRACTIONf_plane_restr0.0027459
X-RAY DIFFRACTIONf_dihedral_angle_d7.57222071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.50.29971340.26292548X-RAY DIFFRACTION98.86
2.5-2.690.26471360.23952586X-RAY DIFFRACTION100
2.69-2.960.28831370.21682613X-RAY DIFFRACTION100
2.96-3.390.23211380.212607X-RAY DIFFRACTION99.82
3.39-4.270.28491390.18762634X-RAY DIFFRACTION98.3
4.27-31.550.23141510.18492846X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 2.74466670686 Å / Origin y: 32.5396989643 Å / Origin z: -26.5986527754 Å
111213212223313233
T0.242881393191 Å20.00585294473349 Å20.000274829507701 Å2-0.349197804865 Å2-0.042141113114 Å2--0.307763121686 Å2
L0.541401723227 °2-0.223425593285 °20.231950311005 °2-0.798674953879 °2-0.470714335489 °2--1.45534921549 °2
S0.0484135343431 Å °0.0834986305095 Å °-0.014091430075 Å °-0.0265794132674 Å °-0.0414115380799 Å °-0.159258827149 Å °0.138266708429 Å °0.292844148882 Å °0.00713109210752 Å °
Refinement TLS groupSelection details: all

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