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Yorodumi- PDB-5lpj: Crystal structure of the bromodomain of human CREBBP bound to the... -
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-Basic information
Entry | Database: PDB / ID: 5lpj | ||||||
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Title | Crystal structure of the bromodomain of human CREBBP bound to the inhibitor XDM1 | ||||||
Components | CREB-binding protein | ||||||
Keywords | TRANSCRIPTION / bromodomain / protein-inhibitor complex / epigenetics | ||||||
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 / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / 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 / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / 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 / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Transcriptional and post-translational regulation of MITF-M expression and activity / Attenuation phase / cellular response to nutrient levels / canonical NF-kappaB signal transduction / 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 / PPARA activates gene expression / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / chromatin DNA binding / p53 binding / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of protein localization to nucleus / rhythmic process / transcription corepressor activity / cellular response to UV / Circadian Clock / HATs acetylate histones / TRAF3-dependent IRF activation pathway / DNA-binding transcription factor binding / transcription regulator complex / protein-containing complex assembly / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / response to hypoxia / nuclear body / chromatin binding / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Huegle, M. / Wohlwend, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles. Authors: Hugle, M. / Lucas, X. / Ostrovskyi, D. / Regenass, P. / Gerhardt, S. / Einsle, O. / Hau, M. / Jung, M. / Breit, B. / Gunther, S. / Wohlwend, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lpj.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lpj.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lpj_validation.pdf.gz | 711.3 KB | Display | wwPDB validaton report |
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Full document | 5lpj_full_validation.pdf.gz | 711.9 KB | Display | |
Data in XML | 5lpj_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 5lpj_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/5lpj ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lpj | HTTPS FTP |
-Related structure data
Related structure data | 5lpkC 5lplC 5lpmC 5nrwC 5nu3C 5nu5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14223.349 Da / Num. of mol.: 1 / Fragment: bromodomain, UNP residues 1081-1197 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase |
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#2: Chemical | ChemComp-XDM / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % / Mosaicity: 0.35 ° |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6.5 / Details: LiSO4, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2014 |
Radiation | Monochromator: Fixed-exit LN2 cooled Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→49.25 Å / Num. obs: 34576 / % possible obs: 93.2 % / Redundancy: 11 % / Biso Wilson estimate: 17.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.268 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.27→1.29 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.788 / % possible all: 20 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo-CBP Resolution: 1.65→42.041 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.16 Å2 / Biso mean: 24.7367 Å2 / Biso min: 11.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→42.041 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -21.9409 Å / Origin y: 52.1717 Å / Origin z: 6.9019 Å
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Refinement TLS group |
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