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- PDB-2mwa: NMR structure of FBP28 WW2 mutant Y446L -

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Basic information

Entry
Database: PDB / ID: 2mwa
TitleNMR structure of FBP28 WW2 mutant Y446L
ComponentsTranscription elongation regulator 1
KeywordsTRANSCRIPTION / melting
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, model1
AuthorsMacias, M.J. / Scheraga, H. / Sunol, D. / Todorovski, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.
Authors: Zhou, R. / Maisuradze, G.G. / Sunol, D. / Todorovski, T. / Macias, M.J. / Xiao, Y. / Scheraga, H.A. / Czaplewski, C. / Liwo, A.
History
DepositionNov 3, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: 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 / 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

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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)4,3151
Polymers4,3151
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 #1lowest energy

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Components

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


Mass: 4314.694 Da / Num. of mol.: 1 / Fragment: WW 2 domain residues 430-466 / Mutation: Y446L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA150, TAF2S, TCERG1 / Production host: Escherichia coli (E. coli) / 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: 0.7 mM protein, 100 mM sodium chloride, 20 mM sodium phosphate, 1 mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.7 mMentity-11
100 mMsodium chloride-21
20 mMsodium phosphate-31
1 mMsodium azide-41
Sample conditionspH: 6.5 / 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
XEASYBartels et al.chemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 367 / NOE intraresidue total count: 0 / NOE long range total count: 193 / NOE medium range total count: 41 / NOE sequential total count: 133
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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