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- PDB-2mh0: Solution NMR structure of the p300 Taz2:ETAD1 complex -

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Basic information

Entry
Database: PDB / ID: 2mh0
TitleSolution NMR structure of the p300 Taz2:ETAD1 complex
Components
  • Histone acetyltransferase p300
  • Transcription factor E2-alpha
KeywordsTRANSCRIPTION/TRANSFERASE / TRANSCRIPTION-TRANSFERASE complex
Function / homology
Function and homology information


vitamin D response element binding / behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity ...vitamin D response element binding / behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / regulation of tubulin deacetylation / histone H2B acetyltransferase activity / bHLH transcription factor binding / internal protein amino acid acetylation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / thigmotaxis / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / positive regulation of TORC2 signaling / immunoglobulin V(D)J recombination / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / cellular response to L-leucine / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / mitogen-activated protein kinase kinase kinase binding / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / TGFBR3 expression / positive regulation by host of viral transcription / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / 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 / face morphogenesis / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / platelet formation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / megakaryocyte development / protein-lysine-acetyltransferase activity / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / B cell lineage commitment / Myogenesis / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase activity / acetyltransferase activity / PI5P Regulates TP53 Acetylation / FOXO-mediated transcription of cell death genes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / fat cell differentiation / E-box binding / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / regulation of G1/S transition of mitotic cell cycle / RUNX3 regulates p14-ARF / histone acetyltransferase complex / canonical NF-kappaB signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / NF-kappaB binding / negative regulation of gluconeogenesis / cellular response to nutrient levels / somitogenesis / negative regulation of protein-containing complex assembly / pre-mRNA intronic binding / Attenuation phase / positive regulation of T-helper 17 cell lineage commitment / 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
Similarity search - Function
: / CREB-binding Protein; Chain A / TAZ domain / Helix-loop-helix DNA-binding 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 ...: / CREB-binding Protein; Chain A / TAZ domain / Helix-loop-helix DNA-binding 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 / : / Histone acetyltransferase p300-like, PHD domain / 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 / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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
Transcription factor E2-alpha / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsLangelaan, D.N. / Smith, S.P. / Chitayat, S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural insights into TAZ2 domain-mediated CBP/p300 recruitment by transactivation domain 1 of the lymphopoietic transcription factor E2A.
Authors: Lochhead, M.R. / Brown, A.D. / Kirlin, A.C. / Chitayat, S. / Munro, K. / Findlay, J.E. / Baillie, G.S. / LeBrun, D.P. / Langelaan, D.N. / Smith, S.P.
History
DepositionNov 12, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor E2-alpha
B: Histone acetyltransferase p300


Theoretical massNumber of molelcules
Total (without water)14,3762
Polymers14,3762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Transcription factor E2-alpha / Class B basic helix-loop-helix protein 21 / bHLHb21 / Immunoglobulin enhancer-binding factor ...Class B basic helix-loop-helix protein 21 / bHLHb21 / Immunoglobulin enhancer-binding factor E12/E47 / Immunoglobulin transcription factor 1 / Kappa-E2-binding factor / Transcription factor 3 / TCF-3 / Transcription factor ITF-1


Mass: 4267.926 Da / Num. of mol.: 1 / Fragment: Activation domain 1 (ETAD1), E2A residues 1-37
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCF3, BHLHB21, E2A, ITF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15923
#2: Protein Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300


Mass: 10107.916 Da / Num. of mol.: 1 / Fragment: TAZ-type 2 zinc finger residues 1723-1812 / Mutation: C1738A, C1746A, C1789A, C1790A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09472, histone acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HCACO
1613D 1H-15N NOESY
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11022D 1H-15N HSQC
11123D HNCO
11223D HCACO
11323D HN(CA)CB
11423D CBCA(CO)NH
11523D 1H-15N NOESY
11623D (H)CCH-TOCSY
11723D 1H-13C NOESY aliphatic
11823D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM [U-99% 13C; U-99% 15N] ETAD1, 2 mM Taz2, 20 mM MES, 1 mM sodium azide, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
23078 uM ETAD1, 1038 uM [U-99% 13C; U-99% 15N] Taz2, 20 mM MES, 1 mM sodium azide, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMETAD1-1[U-99% 13C; U-99% 15N]1
2 mMTaz2-21
20 mMMES-31
1 mMsodium azide-41
5 mMbeta-mercaptoethanol-51
3078 uMETAD1-62
1038 uMTaz2-7[U-99% 13C; U-99% 15N]2
20 mMMES-82
1 mMsodium azide-92
5 mMbeta-mercaptoethanol-102
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
Analysis3CCPNchemical shift assignment
Analysis3CCPNpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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