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- PDB-3t92: Crystal structure of the Taz2:C/EBPepsilon-TAD chimera protein -

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Entry
Database: PDB / ID: 3t92
TitleCrystal structure of the Taz2:C/EBPepsilon-TAD chimera protein
ComponentsHISTONE ACETYLTRANSFERASE P300 TAZ2-CCAAT/ENHANCER-BINDING PROTEIN EPSILON
KeywordsTRANSFERASE / Taz2 domain / zinc finger / transcription / 300/CBP / C/EBP proteins
Function / homology
Function and homology information


cytokine production => GO:0001816 / behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming ...cytokine production => GO:0001816 / behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / granulocyte differentiation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / NOTCH2 intracellular domain regulates transcription / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / chromatin => GO:0000785 / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / cellular response to L-leucine / internal peptidyl-lysine acetylation / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / STAT3 nuclear events downstream of ALK signaling / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / Polo-like kinase mediated events / 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 / regulation of androgen receptor signaling pathway / NFE2L2 regulating MDR associated enzymes / positive regulation by host of viral transcription / regulation of mitochondrion organization / face morphogenesis / 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 / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / nuclear androgen receptor binding / megakaryocyte development / TRAF6 mediated IRF7 activation / regulation of tubulin deacetylation / macrophage derived foam cell differentiation / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / internal protein amino acid acetylation / STAT family protein binding / acyltransferase activity / fat cell differentiation / protein acetylation / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of transforming growth factor beta receptor signaling pathway / PI5P Regulates TP53 Acetylation / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / cellular response to nutrient levels / RUNX3 regulates p14-ARF / macrophage differentiation / NF-kappaB binding / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / Attenuation phase / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / somitogenesis / phagocytosis / pre-mRNA intronic binding / regulation of cellular response to heat / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / skeletal muscle tissue development / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation / positive regulation of TORC1 signaling / RORA activates gene expression / CD209 (DC-SIGN) signaling / negative regulation of autophagy / B cell differentiation
Similarity search - Function
CREB-binding Protein; Chain A / TAZ domain / CCAAT/enhancer-binding protein, chordates / Basic region leucine zipper / 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 ...CREB-binding Protein; Chain A / TAZ domain / CCAAT/enhancer-binding protein, chordates / Basic region leucine zipper / 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. / Coactivator CBP, KIX domain superfamily / Basic-leucine zipper (bZIP) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / basic region leucin zipper / Histone acetylation protein / Basic-leucine zipper domain / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETONE / 3,3',3''-phosphanetriyltripropanoic acid / Histone acetyltransferase p300 / CCAAT/enhancer-binding protein epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBhaumik, P. / Maria, M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014
Title: Structural insights into interactions of C/EBP transcriptional activators with the Taz2 domain of p300.
Authors: Bhaumik, P. / Davis, J. / Tropea, J.E. / Cherry, S. / Johnson, P.F. / Miller, M.
History
DepositionAug 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
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 / _entity.formula_weight
Revision 1.4Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE ACETYLTRANSFERASE P300 TAZ2-CCAAT/ENHANCER-BINDING PROTEIN EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1107
Polymers13,4431
Non-polymers6686
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.860, 47.860, 104.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HISTONE ACETYLTRANSFERASE P300 TAZ2-CCAAT/ENHANCER-BINDING PROTEIN EPSILON / p300 HAT / E1A-associated protein p300


Mass: 13442.639 Da / Num. of mol.: 1 / Fragment: unp residues 1723-1818; unp residues 37-61 / Mutation: C1738A, C1746A, C1789A, C1790A,
Source method: isolated from a genetically manipulated source
Details: p300 HAT/CEBPE / Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Plasmid: pJT153 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus(DE3)-RIL
References: UniProt: Q09472, UniProt: Q15744, histone acetyltransferase

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ACN / ACETONE / Acetone


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 277 K / Method: micro batch under oil / pH: 8.5
Details: 200mM NaCl, 5mM TCEP and 20% isopropanol, pH 8.5, Micro batch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 21587 / Num. obs: 20897 / % possible obs: 96.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3755 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MrBUMPphasing
REFMAC5.5.0104refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.364 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1045 5 %RANDOM
Rwork0.17777 ---
obs0.18024 19850 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.566 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 34 169 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022974
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9941316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5075132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73224.41943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26915194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.925158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021718
X-RAY DIFFRACTIONr_mcbond_it0.8121.5598
X-RAY DIFFRACTIONr_mcangle_it1.4522969
X-RAY DIFFRACTIONr_scbond_it2.5283376
X-RAY DIFFRACTIONr_scangle_it4.1614.5337
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 79 -
Rwork0.263 1503 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8752-2.2681-1.42293.99411.88453.2118-0.1529-0.1510.03470.10140.06520.2226-0.00390.00410.08770.04950.0178-0.01210.0408-0.01860.1071-0.70629.1451.681
216.4103-7.86187.86316.4237-4.39186.2453-0.1765-0.00030.16920.31830.0271-0.1034-0.22960.05370.14950.126-0.00570.00520.0111-0.01740.041618.9355.0412.415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 88
2X-RAY DIFFRACTION2A89 - 119

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