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- PDB-6bgh: Solution NMR structure of Brd3 ET domain bound to Brg1 peptide -

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Basic information

Entry
Database: PDB / ID: 6bgh
TitleSolution NMR structure of Brd3 ET domain bound to Brg1 peptide
Components
  • Brd3_ET
  • Bromodomain-containing protein 3
KeywordsTRANSCRIPTION / Transcription Bromodomain BET protein
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding ...positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / RNA polymerase I preinitiation complex assembly / lncRNA binding / positive regulation by host of viral transcription / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / endodermal cell differentiation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / protein localization to chromatin / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / molecular condensate scaffold activity / helicase activity / transcription coregulator binding / positive regulation of cell differentiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / nuclear matrix / positive regulation of miRNA transcription / transcription corepressor activity / positive regulation of DNA-binding transcription factor activity / p53 binding / nervous system development / positive regulation of cold-induced thermogenesis / chromatin organization / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / helicase superfamily c-terminal domain / Bromodomain / Bromodomain-like superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Transcription activator BRG1 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSzyszka, T.N. / Wai, D.C. / Mackay, J.P.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators.
Authors: Wai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L.E. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Chalmers, J.D. / Patrick, W.M. / Lu, B. / ...Authors: Wai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L.E. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Chalmers, J.D. / Patrick, W.M. / Lu, B. / Vakoc, C.R. / Blobel, G.A. / Mackay, J.P.
History
DepositionOct 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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_nmr_spectrometer.model
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Brd3_ET


Theoretical massNumber of molelcules
Total (without water)11,5972
Polymers11,5972
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 3 / / RING3-like protein


Mass: 10179.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Protein/peptide Brd3_ET


Mass: 1417.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P51532*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
313isotropic22D 1H-13C HSQC
323isotropic23D 1H-13C NOESY
232isotropic23D 1H-15N NOESY
343isotropic23D 13C/15N (F2/F1) Filtered, 1H-1H NOESY
353isotropic12D 13C/15N (F2/F1) Filtered, 1H-1H NOESY
363isotropic12D 13C/15N (F2/F1) Filtered, 1H-1H TOCSY
373isotropic23D (H)CCH-TOCSY
383isotropic23D (H)CCH-COSY
191isotropic22D 1H-1H TOCSY
1101isotropic12D 1H-1H NOESY
3113isotropic13D HNCO
2122isotropic12D 1H-15N HSQC
3133isotropic13D HN(CA)CO
3143isotropic13D H(CC)(CO)HN
3153isotropic13D HNCA
3163isotropic13D CBCA(CO)NH
3173isotropic13D HN(CA)CB

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2OUnlabelled90% H2O/10% D2O
solution2300 uM [U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O15N_Sample90% H2O/10% D2O
solution3300 uM [U-13C; U-15N] Brd3_ET, 600 uM Brg1, 0.02 % Roche Complete Protease Inhibitor, 166 uM DSS, 90% H2O/10% D2O15N_13C_Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMBrd3_ETnatural abundance1
600 uMBrg1natural abundance1
0.02 %Roche Complete Protease Inhibitornatural abundance1
166 uMDSSnatural abundance1
300 uMBrd3_ET[U-15N]2
600 uMBrg1natural abundance2
0.02 %Roche Complete Protease Inhibitornatural abundance2
166 uMDSSnatural abundance2
300 uMBrd3_ET[U-13C; U-15N]3
600 uMBrg1natural abundance3
0.02 %Roche Complete Protease Inhibitornatural abundance3
166 uMDSSnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 NaCl mMUnlabelled7 1 atm298 K
250 NaCl mM15N_Sample7 1 atm298 K
350 NaCl mM13C_15N_Sample7 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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