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- PDB-7xij: Crystal structure of CBP bromodomain liganded with Y08175 -

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Basic information

Entry
Database: PDB / ID: 7xij
TitleCrystal structure of CBP bromodomain liganded with Y08175
ComponentsIsoform 2 of CREB-binding protein
KeywordsPROTEIN BINDING / Histone acetyltransferase / CBP / Bromodomain
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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-EJ3 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsXiang, Q. / Wang, C. / Wu, T. / Zhang, Y. / Zhang, C. / Luo, G. / Wu, X. / Shen, H. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22007088 China
CitationJournal: To Be Published
Title: Crystal structure of CBP bromodomain liganded with Y08175
Authors: Xiang, Q. / Wang, C. / Wu, T. / Zhang, Y. / Zhang, C. / Luo, G. / Wu, X. / Shen, H. / Xu, Y.
History
DepositionApr 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Isoform 2 of CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9895
Polymers16,2771
Non-polymers7134
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-1 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.890, 56.890, 80.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1337-

HOH

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Components

#1: Protein Isoform 2 of CREB-binding protein / Histone lysine acetyltransferase CREBBP / Protein-lysine acetyltransferase CREBBP


Mass: 16276.603 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, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-EJ3 / 3-[(1-ethanoyl-5-methoxy-indol-3-yl)carbonylamino]-4-fluoranyl-5-(1-methylpyrazol-4-yl)benzoic acid


Mass: 450.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19FN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2 0.1M TrsHCl 30% PEG4000 PH7.5

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Data collection

DiffractionMean temperature: 197 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97736 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97736 Å / Relative weight: 1
ReflectionResolution: 1.82→80.62 Å / Num. obs: 14087 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Net I/σ(I): 17.9 / Num. measured all: 101099 / Scaling rejects: 104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.82-1.867.50.24461548200.9830.0940.2626.5100
9.09-80.626.50.0399361450.9980.0160.0422899.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYX

4nyx


Resolution: 1.82→49.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.69 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 793 5.6 %RANDOM
Rwork0.193 ---
obs0.1946 13263 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.71 Å2 / Biso mean: 27.716 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å2-0 Å2
3----2.07 Å2
Refinement stepCycle: final / Resolution: 1.82→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 49 93 1245
Biso mean--33.18 33.51 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191186
X-RAY DIFFRACTIONr_bond_other_d0.0020.021059
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9961605
X-RAY DIFFRACTIONr_angle_other_deg0.9773.0062462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9965130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75724.09861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36515198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.465157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
LS refinement shellResolution: 1.82→1.865 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.352 72 -
Rwork0.208 928 -
obs--100 %

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