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- PDB-6bgg: Solution NMR structures of the BRD3 ET domain in complex with a C... -

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Basic information

Entry
Database: PDB / ID: 6bgg
TitleSolution NMR structures of the BRD3 ET domain in complex with a CHD4 peptide
Components
  • Bromodomain-containing protein 3
  • CHD4
KeywordsPROTEIN BINDING / transcription regulation / epigenetics
Function / homology
Function and homology information


cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / lncRNA binding / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / endodermal cell differentiation ...cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / lncRNA binding / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / endodermal cell differentiation / site of DNA damage / RNA Polymerase I Transcription Initiation / protein localization to chromatin / Regulation of TP53 Activity through Acetylation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / helicase activity / Regulation of PTEN gene transcription / molecular condensate scaffold activity / HDACs deacetylate histones / transcription coregulator binding / double-strand break repair via homologous recombination / lysine-acetylated histone binding / histone deacetylase binding / RNA polymerase II transcription regulator complex / transcription corepressor activity / chromatin organization / histone binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) / DUF1087 / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Chromo-like domain superfamily / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / 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 / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 4 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Lu, B. ...Wai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Lu, B. / Vakoc, C.R. / Blobel, G.A. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
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 1.1Apr 4, 2018Group: Data collection / 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 1.2May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHD4
B: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)11,9622
Polymers11,9622
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Surface plasmon resonance binding assays confirm association of CHD4 peptide with BRD3 ET domain.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area990 Å2
ΔGint-3 kcal/mol
Surface area7330 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CHD4 /


Mass: 1273.629 Da / Num. of mol.: 1 / Fragment: unp residues 290-301 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14839*PLUS
#2: Protein Bromodomain-containing protein 3 / / RING3-like protein


Mass: 10687.956 Da / Num. of mol.: 1 / Fragment: unp residues 557-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q15059

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-15N NOESY
132isotropic13D 1H-13C (F1)-filtered NOESY aliphatic
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HBHA(CO)NH
171isotropic13D HNCO
181isotropic1HN(CA)CO
192isotropic13D (H)CCH-TOCSY
1101isotropic13D H(CCO)NH
1111isotropic12D 15N13C (F2,F1)-filtered) 1H-1H NOESY
1121isotropic12D 1H-15N HSQC
1133isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM [U-13C; U-15N] BRD3, 500 uM CHD4, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2OBRD3-CHD4 in H2O90% H2O/10% D2O
solution2500 uM [U-13C; U-15N] BRD3, 500 uM CHD4, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 100% D2OBRD3-CHD4 in D2O100% D2O
solution3500 uM BRD3, 500 uM CHD4, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2Ounlabelled BRD3-CHD490% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMBRD3[U-13C; U-15N]1
500 uMCHD4natural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
500 uMBRD3[U-13C; U-15N]2
500 uMCHD4natural abundance2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
500 uMBRD3natural abundance3
500 uMCHD4natural abundance3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
Sample conditionsIonic strength: .2 M / Label: 298 K pH 6.5 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.1.3Goddardchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky3.1.3Goddardpeak picking
TopSpin3.5.6Bruker Biospinprocessing
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Water refinement using RECOORD protocol (Nederveen 2015)
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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