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- PDB-5eng: Crystal structure of the bromodomain of human CREBBP in complex w... -

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Basic information

Entry
Database: PDB / ID: 5eng
TitleCrystal structure of the bromodomain of human CREBBP in complex with UP39
ComponentsCREB-binding protein
KeywordsTRANSFERASE / Transcription / INHIBITOR
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / histone lactyltransferase (CoA-dependent) activity / N-terminal peptidyl-lysine acetylation / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / histone lactyltransferase (CoA-dependent) activity / N-terminal peptidyl-lysine acetylation / regulation of smoothened signaling pathway / 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 / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / protein-lysine-acetyltransferase activity / embryonic digit morphogenesis / protein acetylation / homeostatic process / Notch-HLH transcription pathway / histone acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / acetyltransferase activity / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / canonical NF-kappaB signal transduction / 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 / Attenuation phase / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / regulation of cellular response to heat / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / : / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / transcription coactivator binding / Heme signaling / Formation of the beta-catenin:TCF transactivating complex / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / protein destabilization / Evasion by RSV of host interferon responses / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / 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 / : / rhythmic process / HATs acetylate histones / TRAF3-dependent IRF activation pathway / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression
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-5QN / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsDong, 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
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 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)14,6912
Polymers14,2231
Non-polymers4681
Water3,441191
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.237, 49.710, 80.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-5QN / methyl 2-[2-(3,5-dihydro-2~{H}-pyrazin-4-yl)ethoxy]-5-[(5-ethanoyl-2-ethoxy-phenyl)carbamoyl]benzoate


Mass: 467.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29N3O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M KSCN, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.3→42.273 Å / Num. all: 34079 / Num. obs: 34079 / % possible obs: 98.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 10.98 Å2 / Rpim(I) all: 0.012 / Rrim(I) all: 0.033 / Rsym value: 0.031 / Net I/av σ(I): 12.803 / Net I/σ(I): 33.2 / Num. measured all: 230177
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.3-1.375.50.1624.42572546720.0740.1629.594.4
1.37-1.456.90.1186.13142345850.0470.11813.998.1
1.45-1.556.70.0858.32948544160.0350.08518.799.5
1.55-1.687.10.06410.92942941290.0250.06425.1100
1.68-1.846.90.04814.32637337970.0190.04832.299.6
1.84-2.067.30.03717.72548634720.0140.03743.8100
2.06-2.376.90.02921.52119630730.0120.02953.699.8
2.37-2.917.20.02623.11910626420.010.02662.399.9
2.91-4.116.70.02325.11393120660.0090.0237199.6
4.11-40.1736.50.02124.4802312270.0090.02170.899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.3 Å40.17 Å
Translation5.35 Å40.17 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
PHENIXrefinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NR5

4nr5


Resolution: 1.3→40.173 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 1743 5.12 %
Rwork0.1641 32283 -
obs0.1645 34026 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.77 Å2 / Biso mean: 15.1463 Å2 / Biso min: 5.08 Å2
Refinement stepCycle: final / Resolution: 1.3→40.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 34 191 1187
Biso mean--27.48 25.12 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081104
X-RAY DIFFRACTIONf_angle_d1.1131512
X-RAY DIFFRACTIONf_chiral_restr0.079152
X-RAY DIFFRACTIONf_plane_restr0.008199
X-RAY DIFFRACTIONf_dihedral_angle_d20.74446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.33830.17631270.16782492261992
1.3383-1.38150.1981430.16822581272496
1.3815-1.43080.17531450.15992606275197
1.4308-1.48810.17561370.15412679281699
1.4881-1.55580.1531550.143726712826100
1.5558-1.63790.15531360.148327002836100
1.6379-1.74050.16141290.15127182847100
1.7405-1.87490.15731400.162427032843100
1.8749-2.06360.17051530.162627392892100
2.0636-2.36210.1731630.159527232886100
2.3621-2.97590.18051570.178527682925100
2.9759-40.19220.17581580.16882903306199

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