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- PDB-5owk: Crystal structure of CREBBP bromodomain complexed with DSPB2A002 -

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Basic information

Entry
Database: PDB / ID: 5owk
TitleCrystal structure of CREBBP bromodomain complexed with DSPB2A002
ComponentsCREB-binding protein
KeywordsTRANSCRIPTION / CREBBP bromodomain / Inhibitor
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / embryonic digit morphogenesis / homeostatic process / protein acetylation / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / acetyltransferase activity / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase complex / Attenuation phase / regulation of cellular response to heat / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Cytoprotection by HMOX1 / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / Circadian Clock / p53 binding / TRAF3-dependent IRF activation pathway / HATs acetylate histones / protein-containing complex assembly / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / damaged DNA binding / transcription coactivator activity / nuclear body / response to hypoxia / chromatin binding / regulation of DNA-templated transcription / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7MX / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsZhu, J. / Spiliotopoulos, D. / Caflisch, A.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules.
Authors: Zhu, J. / Dong, J. / Batiste, L. / Unzue, A. / Dolbois, A. / Pascanu, V. / Sledz, P. / Nevado, C. / Caflisch, A.
History
DepositionSep 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6553
Polymers14,2231
Non-polymers4312
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.337, 45.073, 61.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CREB-binding protein


Mass: 14223.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-7MX / ethyl 4-chloranyl-1-methyl-6-oxidanylidene-pyridine-3-carboxylate


Mass: 215.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10ClNO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH6.5, 0.1 M MgCl2, 20% PEG6K, 10% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999989 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.25→45.07 Å / Num. obs: 33757 / % possible obs: 97.9 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.8
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.089 / Num. unique obs: 1613 / CC1/2: 0.951 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DWY

3dwy


Resolution: 1.25→36.281 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 15.47
RfactorNum. reflection% reflection
Rfree0.1761 2007 5.96 %
Rwork0.1621 --
obs0.1629 33674 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→36.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 28 229 1211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051027
X-RAY DIFFRACTIONf_angle_d0.9551400
X-RAY DIFFRACTIONf_dihedral_angle_d24.631399
X-RAY DIFFRACTIONf_chiral_restr0.075143
X-RAY DIFFRACTIONf_plane_restr0.007183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28130.17951420.16242181X-RAY DIFFRACTION96
1.2813-1.31590.19131430.15992189X-RAY DIFFRACTION96
1.3159-1.35460.1811360.16372226X-RAY DIFFRACTION97
1.3546-1.39840.15541400.16132243X-RAY DIFFRACTION97
1.3984-1.44840.17051380.15382233X-RAY DIFFRACTION98
1.4484-1.50630.18611470.15232245X-RAY DIFFRACTION98
1.5063-1.57490.17661390.1512275X-RAY DIFFRACTION98
1.5749-1.65790.15991450.14562278X-RAY DIFFRACTION98
1.6579-1.76180.16971460.14762276X-RAY DIFFRACTION98
1.7618-1.89780.17141440.1542250X-RAY DIFFRACTION97
1.8978-2.08880.1841420.15782255X-RAY DIFFRACTION97
2.0888-2.3910.15631440.15752319X-RAY DIFFRACTION99
2.391-3.01220.17571510.17072342X-RAY DIFFRACTION98
3.0122-36.29640.19121500.1772355X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 1.5906 Å / Origin y: 16.4496 Å / Origin z: 64.6817 Å
111213212223313233
T0.0489 Å20.0014 Å2-0.0022 Å2-0.0544 Å2-0.0108 Å2--0.0515 Å2
L0.6054 °2-0.1087 °2-0.2848 °2-0.4107 °20.3276 °2--0.4629 °2
S0.0123 Å °0.0671 Å °-0.0313 Å °-0.0215 Å °-0.0204 Å °-0.0058 Å °-0.0315 Å °-0.0196 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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