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- PDB-2g4a: Solution structure of a Bromodomain from RING3 protein -

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Basic information

Entry
Database: PDB / ID: 2g4a
TitleSolution structure of a Bromodomain from RING3 protein
ComponentsBromodomain-containing protein 2
KeywordsGENE REGULATION / RING3 Bromodomain
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / 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
Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics torsion angle dynamics
Model type detailsminimized average
AuthorsHuang, H. / Wu, J. / Shi, Y.
CitationJournal: to be published
Title: Solution structure of a Bromodomain from RING3
Authors: Huang, H. / Wu, J. / Shi, Y.
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 2


Theoretical massNumber of molelcules
Total (without water)13,8841
Polymers13,8841
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)21 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Bromodomain-containing protein 2 / the RING3 Bromodomain / RING3 protein / O27.1.1


Mass: 13883.900 Da / Num. of mol.: 1 / Fragment: residues 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RING3 / Plasmid: pET22b (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25440

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0mM 15N, 13C-labeled RING3 Bromodomain, 50mM phosphate buffer (pH 5.8), 50mM NaCl, 1mM DTT, 1mM EDTA90% H2O/10% D2O
20.5-1.0mM 15N, 13C-labeled RING3 Bromodomain, 50mM phosphate buffer (pH 5.8), 50mM NaCl, 1mM DTT, 1mM EDTA99.96% D2O
Sample conditionspH: 5.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F.Delaglioprocessing
Sparky3T.D.Goddard and D.G.Knellerdata analysis
CNS1.1structure solution
CSI1David S. Wishartdata analysis
MOLMOL2K.2Koradidata analysis
CNS1.1refinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 21

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