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- PDB-2i7k: Solution Structure of the Bromodomain of Human BRD7 Protein -

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Basic information

Entry
Database: PDB / ID: 2i7k
TitleSolution Structure of the Bromodomain of Human BRD7 Protein
ComponentsBromodomain-containing protein 7
KeywordsTRANSCRIPTION / Helix / Left-handed four-helix bundle
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation / regulation of mitotic cell cycle / positive regulation of cell differentiation / lysine-acetylated histone binding / kinetochore / Wnt signaling pathway / nuclear matrix / transcription corepressor activity / p53 binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / cell cycle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsSun, H. / Liu, J. / Zhang, J. / Huang, H. / Wu, J. / Shi, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Solution structure of BRD7 bromodomain and its interaction with acetylated peptides from histone H3 and H4
Authors: Sun, H. / Liu, J. / Zhang, J. / Shen, W. / Huang, H. / Xu, C. / Dai, H. / Wu, J. / Shi, Y.
History
DepositionAug 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)13,9181
Polymers13,9181
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 / 100The submitted conformer models are the 20 structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 7 / 75 kDa bromodomain protein / Protein CELTIX-1


Mass: 13918.069 Da / Num. of mol.: 1 / Fragment: bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: brain / Gene: BRD7 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NPI1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC
1223D 15N-separated NOESY
132CBCA(CO)NH
142CBCANH
15215N-TOCSY
162HBHA(CBCACO)NH
1723D HNCO
1823D HN(CA)CO
192C(CO)NH-TOCSY
1102H(CCO)NH-TOCSY
11133D 13C-separated NOESY
11233D (H)CCH-TOCSY
11333D (H)CCH-COSY
NMR detailsText: This structure was determined using standard triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM BRD7 bromodomain U-15N; 50mM phosphate buffer (pH 6.1), 50mM NaCl, 1mM DTT, 5mM EDTA; 90% H2O, 10% D2O90% H2O/10% D2O
20.6mM BRD7 bromodomain U-15N,13C; 50mM phosphate buffer (pH 6.1), 50mM NaCl, 1mM DTT, 5mM EDTA; 90% H2O, 10% D2O90% H2O/10% D2O
30.6mM BRD7 bromodomain U-15N,13C; 50mM phosphate buffer (pH 6.1), 50mM NaCl, 1mM DTT, 5mM EDTA; 99.96% D2O99.96% D2O
Sample conditionspH: 6.1 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5brukercollection
NMRPipe2.3Frank Delaglioprocessing
Sparky3.11Goddarddata analysis
CNS1.1refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1871 restraints, 1672 are NOE-derived distance constraints, 115 dihedral angle restraints, 84 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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