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- PDB-2n4r: NMR structure of Fbp28 WW domain L453D mutant -

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Basic information

Entry
Database: PDB / ID: 2n4r
TitleNMR structure of Fbp28 WW domain L453D mutant
ComponentsTranscription elongation regulator 1
KeywordsTRANSCRIPTION / WW domain
Function / homology
Function and homology information


transcription elongation factor activity / RNA polymerase binding / ubiquitin-like protein conjugating enzyme binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity ...transcription elongation factor activity / RNA polymerase binding / ubiquitin-like protein conjugating enzyme binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Transcription elongation regulator 1-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...Transcription elongation regulator 1-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Transcription elongation regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model0
AuthorsMedina, J. / Macias, M. / Martin-Malpartida, P. / Scheraga, H.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Preventing fibril formation of a protein by selective mutation.
Authors: Maisuradze, G.G. / Medina, J. / Kachlishvili, K. / Krupa, P. / Mozolewska, M.A. / Martin-Malpartida, P. / Maisuradze, L. / Macias, M.J. / Scheraga, H.A.
History
DepositionJul 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation regulator 1


Theoretical massNumber of molelcules
Total (without water)4,3671
Polymers4,3671
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 / 300structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide Transcription elongation regulator 1 / TATA box-binding protein-associated factor 2S / Transcription factor CA150


Mass: 4366.640 Da / Num. of mol.: 1 / Mutation: L453D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCERG1, CA150, TAF2S / Plasmid: pGAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O14776

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 500-1000 uM protein, 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
uMentity-1500-10001
25 mMsodium phosphate-21
100 mMsodium chloride-31
Sample conditionspH: 5.8 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVErefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Representative conformer: 1

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