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- PDB-5bt3: Crystal structure of EP300 bromodomain in complex with SGC-CBP30 ... -

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Entry
Database: PDB / ID: 5bt3
TitleCrystal structure of EP300 bromodomain in complex with SGC-CBP30 chemical probe
ComponentsHistone acetyltransferase p300
KeywordsTRANSCRIPTION / p300 / transcription regulation / histone acetyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity ...behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / histone H4 acetyltransferase activity / cellular response to L-leucine / internal peptidyl-lysine acetylation / histone H3 acetyltransferase 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 / acetylation-dependent protein binding / NGF-stimulated transcription / STAT3 nuclear events downstream of ALK signaling / histone H3K18 acetyltransferase activity / Polo-like kinase mediated events / 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 / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / positive regulation by host of viral transcription / face morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / megakaryocyte development / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / regulation of tubulin deacetylation / macrophage derived foam cell differentiation / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / internal protein amino acid acetylation / protein acetylation / fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / PI5P Regulates TP53 Acetylation / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / NF-kappaB binding / histone acetyltransferase complex / Attenuation phase / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / somitogenesis / canonical NF-kappaB signal transduction / positive regulation of T-helper 17 cell lineage commitment / pre-mRNA intronic binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / regulation of cellular response to heat / histone acetyltransferase activity / skeletal muscle tissue development / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Regulation of TP53 Activity through Acetylation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / positive regulation of TORC1 signaling / CD209 (DC-SIGN) signaling / transcription initiation-coupled chromatin remodeling / negative regulation of autophagy / B cell differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / SUMOylation of transcription cofactors / regulation of signal transduction by p53 class mediator / regulation of autophagy
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-2LO / ISOPROPYL ALCOHOL / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsTallant, C. / Hay, D. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Newman, J.A. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Tallant, C. / Hay, D. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Newman, J.A. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of EP300 bromodomain in complex with a 3,5-dimethylisoxazol ligand
Authors: Tallant, C. / Hay, D. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Newman, J.A. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3963
Polymers13,8271
Non-polymers5692
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint3 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.431, 53.431, 77.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300 / EP300


Mass: 13826.797 Da / Num. of mol.: 1 / Fragment: bromodomain, UNP residues 1048-1161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Plasmid: pNIC-Bsa4 / Details (production host): LIC-cloning / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q09472, histone acetyltransferase
#2: Chemical ChemComp-2LO / 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole


Mass: 509.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H33ClN4O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M tri-sodium citrate dihydrate pH 5.6, 20% iso-propanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.05→46.27 Å / Num. all: 604305 / Num. obs: 56052 / % possible obs: 95.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 6.234 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.021 / Net I/av σ(I): 4.6 / Net I/σ(I): 21
Reflection shellResolution: 1.05→1.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.6 / % possible all: 75

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I3J

3i3j


Resolution: 1.05→46.27 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.321 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2776 5 %RANDOM
Rwork0.16498 ---
obs0.1656 53225 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å2-0 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.05→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 40 189 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021049
X-RAY DIFFRACTIONr_bond_other_d0.0050.02982
X-RAY DIFFRACTIONr_angle_refined_deg1.3842.0281432
X-RAY DIFFRACTIONr_angle_other_deg0.9893.0162271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2275119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1924.70651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25615179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.14156
X-RAY DIFFRACTIONr_chiral_restr0.080.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02233
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5280.774467
X-RAY DIFFRACTIONr_mcbond_other0.5150.77466
X-RAY DIFFRACTIONr_mcangle_it0.8671.158586
X-RAY DIFFRACTIONr_mcangle_other0.8681.161587
X-RAY DIFFRACTIONr_scbond_it0.8340.873582
X-RAY DIFFRACTIONr_scbond_other0.8330.873583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3511.266846
X-RAY DIFFRACTIONr_long_range_B_refined3.3457.4891479
X-RAY DIFFRACTIONr_long_range_B_other3.3447.491480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.047→1.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 116 -
Rwork0.241 2619 -
obs--63.62 %

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