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- PDB-2jns: Solution structure of the Bromodomain-containing protein 4 ET domain -

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Basic information

Entry
Database: PDB / ID: 2jns
TitleSolution structure of the Bromodomain-containing protein 4 ET domain
ComponentsBromodomain-containing protein 4
KeywordsUNKNOWN FUNCTION / Bromodomain containing protein 4 / ET-domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / positive regulation of T-helper 17 cell lineage commitment / inner cell mass cell proliferation / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity ...RNA polymerase II C-terminal domain binding / GTP-dependent protein kinase activity / cyclin/CDK positive transcription elongation factor complex / positive regulation of T-helper 17 cell lineage commitment / inner cell mass cell proliferation / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / chromosome segregation / p53 binding / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / : / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / : / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLin, Y.J. / Padmanabhan, B. / Yokoyama, S. / Guntert, P. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the Bromodomain-containing protein 4 ET domain
Authors: Lin, Y.J. / Padmanabhan, B. / Yokoyama, S. / Guntert, P.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: 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: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)10,3231
Polymers10,3231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Bromodomain-containing protein 4 / Mitotic chromosome-associated protein / MCAP


Mass: 10322.638 Da / Num. of mol.: 1 / Fragment: database sequence residues 601-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brd4, Mcap / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ESU6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY

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Sample preparation

DetailsContents: 1.05 mM [U-100% 13C; U-100% 15N] Brd4-ET domain, 100 mM sodium chloride, 20 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.05 mMBrd4-ET domain[U-100% 13C; U-100% 15N]1
100 mMsodium chloride1
20 mMTRIS[U-2H]1
1 mMDTT[U-2H]1
0.02 %sodium azide1
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER DRXBrukerDRX6001
BRUKER AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.2P. Guntert et al.structure solution
CYANA2.2.2P. Guntert et al.refinement
OPALp1.4R. Koradi et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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