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- PDB-7xez: NMR solution structures of p300 TAZ2 domain in complex with BRD4-... -

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Basic information

Entry
Database: PDB / ID: 7xez
TitleNMR solution structures of p300 TAZ2 domain in complex with BRD4-NUT F1c domain binding motif #2
ComponentsHistone acetyltransferase p300,NUT family member 1
KeywordsTRANSFERASE / BRD4-NUT fusion protein / CBP/p300 / TAZ2 domain / F1c domain / NUT carcinoma / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


behavioral defense response / peptidyl-lysine propionylation / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / internal protein amino acid acetylation ...behavioral defense response / peptidyl-lysine propionylation / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / internal protein amino acid acetylation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / histone H4K16 propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / positive regulation of TORC2 signaling / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / 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 / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / acetylation-dependent protein binding / NGF-stimulated transcription / histone lactyltransferase (CoA-dependent) activity / 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 / regulation of glycolytic process / platelet formation / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / megakaryocyte development / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of tubulin deacetylation / protein-lysine-acetyltransferase activity / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / histone acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / PI5P Regulates TP53 Acetylation / fat cell differentiation / acetyltransferase activity / FOXO-mediated transcription of cell death genes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / NF-kappaB binding / negative regulation of gluconeogenesis / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / somitogenesis / 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 / 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
Similarity search - Function
NUT family / Nuclear Testis protein, N-terminal / NUT protein / 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. ...NUT family / Nuclear Testis protein, N-terminal / NUT protein / 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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone acetyltransferase p300 / NUT family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry / simulated annealing
AuthorsYu, D. / Zeng, L. / Zhou, M.-M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770780 China
CitationJournal: Nat Commun / Year: 2023
Title: Structural mechanism of BRD4-NUT and p300 bipartite interaction in propagating aberrant gene transcription in chromatin in NUT carcinoma.
Authors: Yu, D. / Liang, Y. / Kim, C. / Jaganathan, A. / Ji, D. / Han, X. / Yang, X. / Jia, Y. / Gu, R. / Wang, C. / Zhang, Q. / Cheung, K.L. / Zhou, M.M. / Zeng, L.
History
DepositionMar 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.2Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Histone acetyltransferase p300,NUT family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5704
Polymers17,3741
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone acetyltransferase p300,NUT family member 1 / p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone ...p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone crotonyltransferase p300 / Protein 2-hydroxyisobutyryltransferase p300 / Protein lactyltransferas p300 / Protein propionyltransferase p300 / Nuclear protein in testis


Mass: 17373.992 Da / Num. of mol.: 1 / Mutation: C1738A, C1746A, C1789A, C1790A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of p300 (UNP residues 1723-1812), linkers and NUT (UNP residues 419-470)
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300, NUTM1, C15orf55, NUT / Production host: Escherichia coli (E. coli)
References: UniProt: Q09472, UniProt: Q86Y26, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HN(COCA)CB
131isotropic23D 1H-15N NOESY
142isotropic23D 1H-13C NOESY aliphatic
152isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution30.5 mM [U-100% 13C; U-100% 15N] p300 TAZ2 domain in fusion with BRD4-NUT F1c domain binding motif #2, 200 mM sodium phosphate, 3 mM [U-100% 2H] DTT, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution40.5 mM [U-100% 13C; U-100% 15N] p300 TAZ2 domain in fusion with BRD4-NUT F1c domain binding motif #2, 200 mM sodium phosphate, 3 mM [U-100% 2H] DTT, 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMp300 TAZ2 domain in fusion with BRD4-NUT F1c domain binding motif #2[U-100% 13C; U-100% 15N]1
200 mMsodium phosphatenatural abundance1
3 mMDTT[U-100% 2H]1
0.5 mMp300 TAZ2 domain in fusion with BRD4-NUT F1c domain binding motif #2[U-100% 13C; U-100% 15N]2
200 mMsodium phosphatenatural abundance2
3 mMDTT[U-100% 2H]2
Sample conditionsIonic strength units: M / Label: conditions_1 / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinal
distance geometry1
simulated annealing2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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