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- PDB-2ktb: Solution Structure of the Second Bromodomain of Human Polybromo i... -

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Basic information

Entry
Database: PDB / ID: 2ktb
TitleSolution Structure of the Second Bromodomain of Human Polybromo in complex with an acetylated peptide from Histone 3
Components
  • H3_Peptide
  • Protein polybromo-1
KeywordsPROTEIN BINDING / bromodomain / Alternative splicing / Chromatin regulator / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group ...Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsCharlop-Powers, Z. / Zhang, Q. / Zeng, L.
CitationJournal: Cell Res. / Year: 2010
Title: Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2.
Authors: Charlop-Powers, Z. / Zeng, L. / Zhang, Q. / Zhou, M.M.
History
DepositionJan 26, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H3_Peptide
B: Protein polybromo-1


Theoretical massNumber of molelcules
Total (without water)15,9082
Polymers15,9082
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/peptide H3_Peptide


Mass: 2231.602 Da / Num. of mol.: 1 / Fragment: H3(1-20)K14ac / Mutation: K14(ALY) / Source method: obtained synthetically
#2: Protein Protein polybromo-1 / hPB1 / Polybromo-1D / BRG1-associated factor 180 / BAF180


Mass: 13676.723 Da / Num. of mol.: 1 / Fragment: Polybromo Bromdomain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PB1, PBRM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86U86

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 1H-13C NOESY
1213D 1H-15N NOESY
1323D HN(CA)CB
1423D HN(CO)CA
1512D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] Polybromo Bromdomain2, 2.5 mM H3 Peptide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] Polybromo Bromdomain2, 2.5 mM H3 Peptide, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] Polybromo Bromdomain2, 8 mM H3 Peptide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
.5 mMPolybromo Bromdomain2[U-100% 15N]1
2.5 mMH3 Peptide1
.5 mMPolybromo Bromdomain2[U-100% 13C; U-100% 15N]2
2.5 mMH3 Peptide2
.8 mMPolybromo Bromdomain2[U-100% 13C; U-100% 15N]3
8 mMH3 Peptide3
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, J.P. et al.structure solution
CNS2.2Brunger, A.T. et al.refinement
NMRPipeDelaglio, F. et al.processing
NMRViewJohnson, B. et al.chemical shift assignment
RefinementMethod: simulated annealing, torsion angle dynamics / 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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