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- PDB-2nd0: Solution NMR structures of BRD4 ET domain with LANA peptide -

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Basic information

Entry
Database: PDB / ID: 2nd0
TitleSolution NMR structures of BRD4 ET domain with LANA peptide
Components
  • Bromodomain-containing protein 4BRD4
  • LANA
KeywordsTRANSCRIPTION/VIRAL PROTEIN / TRANSCRIPTION / VIRAL PROTEIN / TRANSCRIPTION-VIRAL PROTEIN complex
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / nucleosome binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / viral life cycle / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / nucleosome binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / viral life cycle / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / : / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / host cell nucleus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / : / Protein LANA1-like, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / : / Protein LANA1-like, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
LANA / Bromodomain-containing protein 4 / Protein LANA1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8
MethodSOLUTION NMR / torsion angle dynamics, distance geometry
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 18, 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: LANA


Theoretical massNumber of molelcules
Total (without water)11,8442
Polymers11,8442
Non-polymers00
Water0
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 / BRD4 / 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 LANA


Mass: 2098.506 Da / Num. of mol.: 1 / Fragment: residues 1086-1104 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 8 / References: UniProt: E5LC01, UniProt: Q9QR71*PLUS

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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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
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
TopSpinBruker Biospincollection
ProcheckNMRLaskowski and MacArthurstructure solution
RefinementMethod: torsion angle dynamics, distance geometry / 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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