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- PDB-7jyn: Solution NMR structure of human Brd3 ET complexed with NSD3(148-1... -

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Basic information

Entry
Database: PDB / ID: 7jyn
TitleSolution NMR structure of human Brd3 ET complexed with NSD3(148-184) peptide
Components
  • Bromodomain-containing protein 3
  • Histone-lysine N-methyltransferase NSD3
KeywordsSIGNALING PROTEIN / Brd3 ET / NSD3 solution NMR / Integrase / extra terminal domain
Function / homology
Function and homology information


[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / lncRNA binding / histone H3 methyltransferase activity / endodermal cell differentiation ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / lncRNA binding / histone H3 methyltransferase activity / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / PKMTs methylate histone lysines / methylation / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain / AWS domain ...: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / 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 / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Bromodomain-containing protein 3 / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsAiyer, S. / Swapna, G.V.T. / Roth, M.J. / 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 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 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 / _citation.page_last / _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
B: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)15,5942
Polymers15,5942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The stoichiometry of chain A:chain B is 1:1
TypeNameSymmetry operationNumber
identity operation1_5551
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 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15059
#2: Protein/peptide Histone-lysine N-methyltransferase NSD3 / Nuclear SET domain-containing protein 3 / Protein whistle / WHSC1-like 1 isoform 9 with ...Nuclear SET domain-containing protein 3 / Protein whistle / WHSC1-like 1 isoform 9 with methyltransferase activity to lysine / Wolf-Hirschhorn syndrome candidate 1-like protein 1 / WHSC1-like protein 1


Mass: 4329.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD3, WHSC1L1, DC28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BZ95, Transferases; Transferring one-carbon groups; Methyltransferases
Has ligand of interestY

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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
121isotropic12D 1H-13C HSQC
131isotropic12D HNOE
141isotropic13D HNCO
151isotropic13D HNCA
161isotropic13D HN(CA)CB
1101isotropic13D CBCA(CO)NH
191isotropic13D HBHA(CO)NH
181isotropic13D (H)CCH-TOCSY
171isotropic13D 13C 15N simNOESY
2112isotropic22D 1H-15N HSQC
2302isotropic22D 1H-13C HSQC aliphatic
2292isotropic22D HNOE
2282isotropic23D HNCO
2272isotropic23D HBHA(CO)NH
2262isotropic23D HN(CA)CB
2252isotropic23D CBCA(CO)NH
2242isotropic23D (H)CCH-TOCSY
2232isotropic23D 13C 15N simNOESY
2222isotropic23D 13C edited NOESY aromatic
2212isotropic23D X-filtered NOESY
3203isotropic12D 1H-15N HSQC
3193isotropic12D 1H-13C HSQC
3183isotropic12D HNOE
3173isotropic13D HNCO
3163isotropic13D HNCA
3153isotropic13D HN(CA)CB
3143isotropic13D CBCA(CO)NH
3133isotropic13D HBHA(CO)NH
3123isotropic13D (H)CCH-TOCSY
3313isotropic13D 13C 15N simNOESY
3323isotropic13D 13C edited NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-100% 13C; U-100% 15N] NSD3(148-184), 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O45 uL of peptide with 20 mM Sodium phosphate, 100mM NaCl and 2 mM 2-mercaptoethanol13C_15N_NSD3-148-18490% H2O/10% D2O
solution20.25 mM NSD3(148-184), 0.25 mM U-100% 13C; U-100% 15 Brd3ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O40 uL of peptide with 20 mM Sodium phosphate, 100mM NaCl and 2 mM 2-mercaptoethanol13C_15N_Brd3ET-unNSD3-148-18490% H2O/10% D2O
solution30.25 mM [U-100% 13C; U-100% 15N] NSD3(148-184), 0.2 mM [U-100% 13C; U-100% 15N] Brd3ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O275 uL of peptide with 20 mM Sodium phosphate, 100mM NaCl and 2 mM 2-mercaptoethanol13C_15N_Brd3ET-13C_15N_NSD3-148-18490% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNSD3(148-184)[U-100% 13C; U-100% 15N]1
100 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
2 mM2-mercaptoethanolnatural abundance1
0.25 mMNSD3(148-184)natural abundance2
0.25 mMBrd3ETU-100% 13C; U-100% 152
100 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
2 mM2-mercaptoethanolnatural abundance2
0.25 mMNSD3(148-184)[U-100% 13C; U-100% 15N]3
0.2 mMBrd3ET[U-100% 13C; U-100% 15N]3
100 mMsodium chloridenatural abundance3
20 mMsodium phosphatenatural abundance3
2 mM2-mercaptoethanolnatural abundance3
Sample conditions

Details: 20 mM sodium phosphate, 100mM NaCl and 2 mM 2-mercaptoethanol / Ionic strength: 100 mM 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
113C_15N_NSD3
213C_15N_Brd3ET_unNSD3
313C_15N_Brd3ET_13C_15N_NSD3

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD6001Equipped with 5mm TCI probe
Bruker AVANCEBrukerAVANCE8002equipped with 5mm TXI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.3b, 3.2Bruker Biospincollection
NMRPipe10.8Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.3bBruker Biospinprocessing
AutoAssign2.4Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PINE ServerWoonghee Lee, Arash Bahrami, Hesam Dashti, Hamid R. Eghbalnia, Marco Tonelli, William M. Westler, John L. Markley. (2019) Journal of Biomolecular NMR. 73(5): 213-222.chemical shift assignment
SparkyGoddarddata analysis
ASDP2.3Huang et al.geometry optimization
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardpeak picking
RefinementMethod: distance geometry / Software ordinal: 9
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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