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- PDB-6cui: Solution structure of the Extraterminal (ET) Domain of BRD2 -

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Basic information

Entry
Database: PDB / ID: 6cui
TitleSolution structure of the Extraterminal (ET) Domain of BRD2
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsHouliston, S. / Lemak, A. / Picaud, S. / Filippakopoulos, P. / Arrowsmith, C.H.
CitationJournal: To Be Published
Title: Solution structure of the Extraterminal (ET) Domain of BRD2
Authors: Houliston, S. / Lemak, A. / Picaud, S. / Filippakopoulos, P. / Arrowsmith, C.H.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)15,2751
Polymers15,2751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12540 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 15275.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic23D CBCA(CO)NH
141isotropic23D HNCO
151isotropic23D HBHA(CO)NH
181isotropic23D HNCA
171isotropic12D 1H-15N HSQC
161isotropic12D 1H-13C HSQC aliphatic
191isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution / Contents: 250 uM [U-13C; U-15N] BRD2-ET, 95% H2O/5% D2O / Label: dl-sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 250 uM / Component: BRD2-ET / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 10 mM HEPES, 500 mM NaCl / Ionic strength: 500 mM / Label: Buffer 1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ABACUSLemak and Arrowsmithchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular 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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