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- PDB-6fqo: Crystal structure of CREBBP bromodomain complexd with DT29 -

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Basic information

Entry
Database: PDB / ID: 6fqo
TitleCrystal structure of CREBBP bromodomain complexd with DT29
ComponentsCREB-binding protein
KeywordsTRANSFERASE / Inhibitor / Bromodomain
Function / homology
Function and homology information


NFE2L2 regulating ER-stress associated genes / histone H3K27 acetyltransferase activity / peptide N-acetyltransferase activity / histone H3K18 acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / MRF binding ...NFE2L2 regulating ER-stress associated genes / histone H3K27 acetyltransferase activity / peptide N-acetyltransferase activity / histone H3K18 acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / MRF binding / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / 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 / negative regulation of transcription by RNA polymerase I / 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 / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating anti-oxidant/detoxification enzymes / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / homeostatic process / Notch-HLH transcription pathway / protein acetylation / Formation of paraxial mesoderm / non-canonical NF-kappaB signal transduction / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / 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 / 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 / protein destabilization / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Cytoprotection by HMOX1 / chromatin DNA binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / response to hypoxia / nuclear body / chromatin binding / chromatin / regulation of DNA-templated transcription / 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 / cytosol / cytoplasm
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-E2T / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsZhu, J. / 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
DepositionFeb 14, 2018Deposition 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
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4926
Polymers28,4472
Non-polymers1,0454
Water5,134285
1
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7463
Polymers14,2231
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7463
Polymers14,2231
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.736, 43.664, 51.301
Angle α, β, γ (deg.)90.00, 99.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CREB-binding protein /


Mass: 14223.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-E2T / ~{N}-[3-(2,5-dimethyl-3-oxidanylidene-1,2-oxazol-4-yl)-5-(5-ethanoyl-2-ethoxy-phenyl)phenyl]furan-2-carboxamide


Mass: 460.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24N2O6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.15 M KSCN, 20% PEG3350, 10% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999989 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.35→43.66 Å / Num. obs: 48359 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Net I/σ(I): 26.5
Reflection shellResolution: 1.35→1.374 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.452 / Num. unique obs: 2388 / CC1/2: 0.898 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DWY

3dwy


Resolution: 1.35→38.912 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 2002 4.14 %
Rwork0.1709 --
obs0.1719 48329 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→38.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 76 285 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072113
X-RAY DIFFRACTIONf_angle_d1.1262877
X-RAY DIFFRACTIONf_dihedral_angle_d11.6361335
X-RAY DIFFRACTIONf_chiral_restr0.074290
X-RAY DIFFRACTIONf_plane_restr0.007374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38380.27751370.22083184X-RAY DIFFRACTION96
1.3838-1.42120.22081350.2043210X-RAY DIFFRACTION97
1.4212-1.4630.22461440.19733259X-RAY DIFFRACTION97
1.463-1.51020.19751390.17143255X-RAY DIFFRACTION98
1.5102-1.56420.19531400.16813275X-RAY DIFFRACTION99
1.5642-1.62680.19641400.1613312X-RAY DIFFRACTION100
1.6268-1.70090.20031450.1633317X-RAY DIFFRACTION100
1.7009-1.79060.19331440.16553328X-RAY DIFFRACTION100
1.7906-1.90270.20991420.17243363X-RAY DIFFRACTION100
1.9027-2.04960.19241450.16893332X-RAY DIFFRACTION100
2.0496-2.25590.18241490.15673329X-RAY DIFFRACTION100
2.2559-2.58230.18751430.17033372X-RAY DIFFRACTION100
2.5823-3.25310.18381480.17543363X-RAY DIFFRACTION100
3.2531-38.92860.19121510.16853428X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.1606 Å / Origin y: 0.5657 Å / Origin z: 16.5162 Å
111213212223313233
T0.1005 Å2-0.0063 Å2-0.0012 Å2-0.0844 Å20.0044 Å2--0.0691 Å2
L1.157 °20.1901 °2-0.0902 °2-0.46 °2-0.1122 °2--0.324 °2
S-0.0258 Å °0.1348 Å °0.023 Å °-0.0588 Å °0.025 Å °-0.007 Å °0.0017 Å °0.0103 Å °0.0024 Å °
Refinement TLS groupSelection details: all

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