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- PDB-2nd1: Solution NMR structures of BRD4 ET domain in complex with NSD3_3 ... -

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Basic information

Entry
Database: PDB / ID: 2nd1
TitleSolution NMR structures of BRD4 ET domain in complex with NSD3_3 peptide
Components
  • Bromodomain-containing protein 4
  • Histone-lysine N-methyltransferase NSD3
KeywordsTRANSCRIPTION/TRANSFERASE / Transcription / transferase / TRANSCRIPTION-TRANSFERASE complex
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 / histone H3 methyltransferase activity / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint ...[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 / histone H3 methyltransferase activity / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / PKMTs methylate histone lysines / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / methylation / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / 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. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsZeng, L. / Zhou, M.
CitationJournal: Structure / Year: 2016
Title: Structural Mechanism of Transcriptional Regulator NSD3 Recognition by the ET Domain of BRD4.
Authors: Zhang, Q. / Zeng, L. / Shen, C. / Ju, Y. / Konuma, T. / Zhao, C. / Vakoc, C.R. / Zhou, M.M.
History
DepositionApr 19, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 4
B: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)11,3032
Polymers11,3032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 9745.136 Da / Num. of mol.: 1 / Fragment: residues 601-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#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: 1557.936 Da / Num. of mol.: 1 / Fragment: residues 593-605 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9BZ95, histone-lysine N-methyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D 1H-15N NOESY
1523D 1H-15N TOCSY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic
1812D 1H-13C HSQC
1913D filtered 1H-13C NOESY aliphatic
11013D filtered 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O100% D2O
210 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphate-11
100 mMsodium chloride-21
2 mMDTT-3[U-100% 2H]1
10 mMsodium phosphate-42
100 mMsodium chloride-52
2 mMDTT-6[U-100% 2H]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRView5.04Johnson, One Moon Scientificpeak picking
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
NMRView5.04Johnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpin2.1Bruker Biospincollection
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
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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