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- PDB-9vq1: NMR solution structures of BRD4 ET domain in complex with ASXL1 p... -

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Basic information

Entry
Database: PDB / ID: 9vq1
TitleNMR solution structures of BRD4 ET domain in complex with ASXL1 peptide
Components
  • Bromodomain-containing protein 4
  • Polycomb group protein ASXL1
KeywordsPROTEIN BINDING / ASXL1 / BRD4 / BAP1 / ET domain
Function / homology
Function and homology information


PR-DUB complex / positive regulation of retinoic acid receptor signaling pathway / lung saccule development / podocyte development / negative regulation of peroxisome proliferator activated receptor signaling pathway / regulation of kidney size / nuclear retinoic acid receptor binding / peroxisome proliferator activated receptor binding / bone marrow development / negative regulation of fat cell differentiation ...PR-DUB complex / positive regulation of retinoic acid receptor signaling pathway / lung saccule development / podocyte development / negative regulation of peroxisome proliferator activated receptor signaling pathway / regulation of kidney size / nuclear retinoic acid receptor binding / peroxisome proliferator activated receptor binding / bone marrow development / negative regulation of fat cell differentiation / histone H4K8ac reader activity / histone H3K9ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / hemopoiesis / negative regulation of DNA damage checkpoint / histone H4 reader activity / homeostasis of number of cells / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / positive regulation of G2/M transition of mitotic cell cycle / response to retinoic acid / positive regulation of T-helper 17 cell lineage commitment / heart morphogenesis / RNA polymerase II CTD heptapeptide repeat kinase activity / thymus development / animal organ morphogenesis / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / cell morphogenesis / p53 binding / UCH proteinases / chromosome / chromatin organization / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. ...Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Polycomb group protein ASXL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZeng, L. / Zhou, M.-M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Recruitment of BRD4 to the ASXL1 genomic targets depends on the extra-terminal domain of BRD4
Authors: Selvam, K. / Lu, S. / Messmer, C. / Pang, Y. / Biswas, S. / Khalil, M. / Zhang, P. / Lauberth, S.M. / Tulaiha, R. / Zhou, M.-M. / Lauberth, S.M. / Blanco, M.A. / Yang, F.-C. / Affar, E.B. / ...Authors: Selvam, K. / Lu, S. / Messmer, C. / Pang, Y. / Biswas, S. / Khalil, M. / Zhang, P. / Lauberth, S.M. / Tulaiha, R. / Zhou, M.-M. / Lauberth, S.M. / Blanco, M.A. / Yang, F.-C. / Affar, E.B. / Zhao, Z. / Zeng, L. / Wang, L. / Kutateladze, T.G.
History
DepositionJul 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Polycomb group protein ASXL1


Theoretical massNumber of molelcules
Total (without water)11,4202
Polymers11,4202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 9745.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O60885
#2: Protein/peptide Polycomb group protein ASXL1 / Additional sex combs-like protein 1


Mass: 1675.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IXJ9
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
122isotropic23D 1H-13C NOESY aliphatic
132isotropic23D 1H-13C NOESY aromatic
142isotropic23D 1H-13C filtered-NOESY aliphatic
152isotropic23D 1H-13C filtered-NOESY aromatic
161isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1137 mM sodium chloride, 10 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution2137 mM sodium chloride, 10 mM sodium phosphate, 2 mM DTT, 100% D2O13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
137 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
2 mMDTTnatural abundance1
137 mMsodium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
2 mMDTTnatural abundance2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.4 / 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 Scientificdata analysis
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
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: 200 / Conformers submitted total number: 20

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