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- PDB-7b9x: NMR2 structure of TRIM24-BD in complex with a precursor of IACS-9571 -

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Basic information

Entry
Database: PDB / ID: 7b9x
TitleNMR2 structure of TRIM24-BD in complex with a precursor of IACS-9571
ComponentsTranscription intermediary factor 1-alpha
KeywordsONCOPROTEIN / TRIM24 / bromodomain / IACS-9571 / NMR2
Function / homology
Function and homology information


perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / male germ cell nucleus ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / male germ cell nucleus / nuclear receptor binding / protein catabolic process / lysine-acetylated histone binding / regulation of protein stability / euchromatin / RING-type E3 ubiquitin transferase / response to peptide hormone / ubiquitin protein ligase activity / negative regulation of epithelial cell proliferation / Signaling by BRAF and RAF1 fusions / p53 binding / regulation of apoptotic process / transcription by RNA polymerase II / transcription coactivator activity / protein ubiquitination / protein kinase activity / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / mitochondrion / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger ...B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-T52 / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsOrts, J. / Torres, F. / Milbradt, A.G. / Walser, R.
CitationJournal: J.Med.Chem. / Year: 2022
Title: NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24.
Authors: Torres, F. / Walser, R. / Kaderli, J. / Rossi, E. / Bobby, R. / Packer, M.J. / Sarda, S. / Walker, G. / Hitchin, J.R. / Milbradt, A.G. / Orts, J.
History
DepositionDec 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1942
Polymers12,5781
Non-polymers6161
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6810 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Transcription intermediary factor 1-alpha / TIF1-alpha / E3 ubiquitin-protein ligase TRIM24 / RING finger protein 82 / RING-type E3 ubiquitin ...TIF1-alpha / E3 ubiquitin-protein ligase TRIM24 / RING finger protein 82 / RING-type E3 ubiquitin transferase TIF1-alpha / Tripartite motif-containing protein 24


Mass: 12578.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15164, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-T52 / N-{6-[3-(4-Aminobutoxy)-5-propoxyphenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamide / ~{N}-[6-[3-(4-azanylbutoxy)-5-propoxy-phenoxy]-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl]-3,4-dimethoxy-benzenesulfonamide


Mass: 615.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H39N4O8S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-13C HSQC aliphatic
132isotropic12D 1H-1H COSY
142isotropic12D 1H-1H NOESY
152isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.1 mM [U-13C; U-15N] TRIM24-BD, 50 mM [U-2H] HEPES, 100 mM sodium chloride, 1 mM TCEP, 10 % [U-2H] D2O, 1.1 mM N-{6-[3-(4-Aminobutoxy)-5-propoxyphenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamide, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution250 mM [U-2H] HEPES, 100 mM sodium chloride, 1 mM TCEP, 10 % [U-2H] D2O, 1.1 % N-{6-[3-(4-Aminobutoxy)-5-propoxyphenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamide, 90% H2O/10% D2Oligand_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMTRIM24-BD[U-13C; U-15N]1
50 mMHEPES[U-2H]1
100 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
10 %D2O[U-2H]1
1.1 mMN-{6-[3-(4-Aminobutoxy)-5-propoxyphenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamidenatural abundance1
50 mMHEPES[U-2H]2
100 mMsodium chloridenatural abundance2
1 mMTCEPnatural abundance2
10 %D2O[U-2H]2
1.1 %N-{6-[3-(4-Aminobutoxy)-5-propoxyphenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamidenatural abundance2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.4 / PH err: 0.05 / Pressure: 1 bar / Temperature: 303 K / Temperature err: 0.25

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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