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- PDB-7jmy: Solution NMR structure of human Brd3 ET domain -

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Basic information

Entry
Database: PDB / ID: 7jmy
TitleSolution NMR structure of human Brd3 ET domain
ComponentsBromodomain-containing protein 3
KeywordsSIGNALING PROTEIN / Integrase / BET proteins / BRD3 / extra-terminal domain
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / regulation of transcription by RNA polymerase II / nucleus
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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAiyer, S. / Swapna, G.V.T. / Roth, J.M. / Montelione, G.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorNIH-MIRA R35GM122518 United States
National Institutes of Health/Office of the DirectorRO1 GM110639 United States
National Institutes of Health/Office of the DirectorGM120574 United States
CitationJournal: Structure / Year: 2021
Title: A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins.
Authors: Aiyer, S. / Swapna, G.V.T. / Ma, L.C. / Liu, G. / Hao, J. / Chalmers, G. / Jacobs, B.C. / Montelione, G.T. / Roth, M.J.
History
DepositionAug 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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

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Assembly

Deposited unit
A: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)11,2651
Polymers11,2651
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1target function

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Components

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


Mass: 11264.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pET15_NESG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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
111isotropic12D 1H-15N HSQC
121isotropic11D T1
131isotropic11D T2
141isotropic12D HNOE
252isotropic22D 1H-15N HSQC
2142isotropic22D 1H-13C HSQC aliphatic
2132isotropic23D HNCO
2122isotropic23D HNCA
2112isotropic23D HN(CA)CB
2102isotropic23D CBCA(CO)NH
292isotropic23D HBHA(CO)NH
282isotropic23D (H)CCH-TOCSY
272isotropic23D 1H-13C,15N simNOESY
262isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-15N] Brd3 ET Domain, 100 mM sodium chloride, 20 mM Na3PO4, 2 mM 2-mercapto ethanol, 90% H2O/10% D2O45 uL of the protein sample with 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol15N_Brd3ET90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] Brd3 ET Domain, 100 mM sodium chloride, 20 mM Na3PO4, 2 mM beta-mercaptoethanol, 90% H2O/10% D2O275 uL of the protein sample with 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol15N_13C_Brd3ET90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMBrd3 ET Domain[U-15N]1
100 mMsodium chloridenatural abundance1
20 mMNa3PO4natural abundance1
2 mM2-mercapto ethanolnatural abundance1
0.5 mMBrd3 ET Domain[U-13C; U-15N]2
100 mMsodium chloridenatural abundance2
20 mMNa3PO4natural abundance2
2 mMbeta-mercaptoethanolnatural abundance2
Sample conditions

Details: 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol / Ionic strength: 100mM NaCl mM / Ionic strength err: 0.2 / pH: 7.0 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.05 / Temperature: 298 K / Temperature err: 0.1

Conditions-IDLabel
115N_Brd3ET
215N_13C_Brd3ET

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Equipped with 1.7mm microcryoprobe
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
AutoAssign2.4Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
ASDP1.2Huang et algeometry optimization
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.3bBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1277 conformationally-restricting NOE-derived distance constraints, 122 dihedral angle constraints, and 38 hydrogen bond constraints (16.3 constraints ...Details: The structures are based on a total of 1277 conformationally-restricting NOE-derived distance constraints, 122 dihedral angle constraints, and 38 hydrogen bond constraints (16.3 constraints per residue excluding tags; 1.8 long range constraints per residue). Structure determination was performed iteratively using CYANA and ASDP (Cyana). The 20 lowest energy structures were further refined by restrained molecular dyanmics/energy minimization in explicit water (CNS).
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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