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- PDB-4whu: BROMO domain of CREB binding protein -

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Basic information

Entry
Database: PDB / ID: 4whu
TitleBROMO domain of CREB binding protein
ComponentsCREB-binding protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / bromo domain / creb binding protein / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / histone H3K18 acetyltransferase activity / regulation of smoothened signaling pathway / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...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 / histone H3K18 acetyltransferase activity / regulation of smoothened signaling pathway / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / 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 FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / 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 / TRAF6 mediated IRF7 activation / FOXO-mediated transcription of cell death genes / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / 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 / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / Attenuation phase / positive regulation of double-strand break repair via homologous recombination / cellular response to nutrient levels / Transcriptional and post-translational regulation of MITF-M expression and activity / canonical NF-kappaB signal transduction / histone acetyltransferase activity / regulation of cellular response to heat / histone acetyltransferase / RORA activates gene expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / transcription coactivator binding / Pre-NOTCH Transcription and Translation / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription corepressor activity / cellular response to UV / p53 binding / Circadian Clock / rhythmic process / 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 / response to hypoxia / nuclear body / 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 / 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-3OT / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsLiu, S.
CitationJournal: To Be Published
Title: Direct photocapture of bromodomains using tropolone chemical probes
Authors: Hett, E.C. / Piatnitski Chekler, E.L. / Basak, A. / Bonin, P.D. / Denny, R.A. / Flick, A.C. / Geoghegan, K.F. / Liu, S. / Pletcher, M.T. / Robinson, R.P. / Sahasrabudhe, P. / Salter, S. / ...Authors: Hett, E.C. / Piatnitski Chekler, E.L. / Basak, A. / Bonin, P.D. / Denny, R.A. / Flick, A.C. / Geoghegan, K.F. / Liu, S. / Pletcher, M.T. / Robinson, R.P. / Sahasrabudhe, P. / Salter, S. / Stock, I.A. / Jones, L.H.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)14,6932
Polymers14,2231
Non-polymers4701
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.284, 43.317, 51.387
Angle α, β, γ (deg.)90.00, 98.68, 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.: 1 / Fragment: UNP residues 1081-1197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-3OT / 2-methoxy-4-{1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazol-5-yl}cyclohepta-2,4,6-trien-1-one


Mass: 469.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: obtained through screen with Hampton Research kits (HT and Index)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: single Wavelenghth
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→32.96 Å / Num. all: 24617 / Num. obs: 6356 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 34.29 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24.6
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.3 / % possible all: 90.9

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DVW

3dvw


Resolution: 2.11→32.96 Å / Cor.coef. Fo:Fc: 0.9361 / Cor.coef. Fo:Fc free: 0.8931 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.288 / SU Rfree Blow DPI: 0.217 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 289 4.56 %RANDOM
Rwork0.2077 ---
obs0.2101 6341 98.69 %-
Displacement parametersBiso mean: 58.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.0197 Å20 Å22.6708 Å2
2--2.1761 Å20 Å2
3----5.1958 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.11→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 35 13 1036
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081087HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.951504HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d378SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes183HARMONIC5
X-RAY DIFFRACTIONt_it1087HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion18.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion124SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1181SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.36 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2813 80 4.61 %
Rwork0.2239 1657 -
all0.2263 1737 -
obs--98.69 %
Refinement TLS params.Method: refined / Details: chain A / Origin x: 5.16 Å / Origin y: 39.0207 Å / Origin z: 10.189 Å
111213212223313233
T0.1312 Å20.1323 Å2-0.0054 Å2--0.0181 Å2-0.035 Å2---0.0599 Å2
L4.9017 °2-2.2277 °20.4999 °2-7.3293 °20.4128 °2--5.6448 °2
S-0.5648 Å °-0.6987 Å °-0.075 Å °1.182 Å °0.2642 Å °0.165 Å °-0.5963 Å °-0.523 Å °0.3006 Å °
Refinement TLS groupSelection details: { A|* }

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