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- PDB-5gh9: Crystal structure of CBP Bromodomain with H3K56ac peptide -

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Basic information

Entry
Database: PDB / ID: 5gh9
TitleCrystal structure of CBP Bromodomain with H3K56ac peptide
Components
  • CREB-binding protein
  • Histone H3
KeywordsTRANSCRIPTION / H3K56ac Bromodomain
Function / homology
Function and homology information


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 H3K27 acetyltransferase activity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / MRF binding ...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 H3K27 acetyltransferase activity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / 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 / positive regulation of transforming growth factor beta receptor signaling pathway / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / acetyltransferase activity / 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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / regulation of cellular response to heat / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / telomere organization / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / CD209 (DC-SIGN) signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / HCMV Late Events / Activation of gene expression by SREBF (SREBP) / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / protein destabilization / Heme signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / Transcriptional activation of mitochondrial biogenesis / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / nucleosome
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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
Histone H3 / Histone H3.1 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsXu, L.
CitationJournal: FEBS J. / Year: 2017
Title: Structural insight into CBP bromodomain-mediated recognition of acetylated histone H3K56ac
Authors: Xu, L. / Cheng, A. / Huang, M. / Zhang, J. / Jiang, Y. / Wang, C. / Li, F. / Bao, H. / Gao, J. / Wang, N. / Liu, J. / Wu, J. / Wong, C.C.L. / Ruan, K.
History
DepositionJun 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)15,9392
Polymers15,9392
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-4 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.826, 45.832, 66.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CREB-binding protein /


Mass: 14217.365 Da / Num. of mol.: 1 / Fragment: UNP residues 1081-1196
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)
Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: Q92793
#2: Protein/peptide Histone H3 /


Mass: 1721.979 Da / Num. of mol.: 1 / Fragment: UNP residues 45-58 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: K7EMV3, UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.23 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M Cadmium sulfate hydrate, 0.1 M HEPES, 1.0 M Sodium acetate trihydrate,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 24495 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 12.93 Å2 / Rmerge(I) obs: 0.061 / Net I/av σ(I): 33.113 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.45-1.535.50.547199.7
1.53-1.555.50.48199.9
1.55-1.585.10.454199.7
1.58-1.625.80.424199.8
1.62-1.656.20.341199.8
1.65-1.696.20.317199.5
1.69-1.736.20.2831100
1.73-1.786.20.234199.4
1.78-1.836.20.187199.7
1.83-1.896.10.155199.8
1.89-1.965.70.128199.5
1.96-2.045.60.101199.8
2.04-2.136.40.081199.9
2.13-2.246.30.066199.9
2.24-2.386.30.058199.9
2.38-2.566.10.05199.7
2.56-2.825.50.042199.2
2.82-3.236.10.036199.9
3.23-4.076.10.0311100
4.07-505.50.03198.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUI

4oui


Resolution: 1.451→37.652 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1764 1199 5.09 %
Rwork0.1454 --
obs0.1469 23538 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→37.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 131 1145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051060
X-RAY DIFFRACTIONf_angle_d0.8351439
X-RAY DIFFRACTIONf_dihedral_angle_d18.567417
X-RAY DIFFRACTIONf_chiral_restr0.074148
X-RAY DIFFRACTIONf_plane_restr0.006189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4508-1.50890.20641150.14912451X-RAY DIFFRACTION99
1.5089-1.57760.21931360.1332448X-RAY DIFFRACTION100
1.5776-1.66070.16921280.12532460X-RAY DIFFRACTION100
1.6607-1.76480.17051320.12812439X-RAY DIFFRACTION99
1.7648-1.9010.17161190.12722492X-RAY DIFFRACTION100
1.901-2.09230.15881350.13392454X-RAY DIFFRACTION99
2.0923-2.3950.15691540.13632480X-RAY DIFFRACTION100
2.395-3.01730.17431500.15742491X-RAY DIFFRACTION99
3.0173-37.66510.19021300.1582624X-RAY DIFFRACTION99

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