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- PDB-2nnt: General structural motifs of amyloid protofilaments -

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Basic information

Entry
Database: PDB / ID: 2nnt
TitleGeneral structural motifs of amyloid protofilaments
ComponentsTranscription elongation regulator 1
KeywordsPROTEIN FIBRIL / fibre / beta-hairpin / FBP28 protofilament / CA150 second WW domain
Function / homology
Function and homology information


transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding / RNA polymerase 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 / ubiquitin-like protein conjugating enzyme binding / RNA polymerase 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)
MethodSOLID-STATE NMR / simulated annealing, molecular dynamics
AuthorsFerguson, N. / Becker, J. / Tidow, H. / Tremmel, S. / Sharpe, T.D. / Krause, G. / Flinders, J. / Petrovich, M. / Berriman, J. / Oschkinat, H. / Fersht, A.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: General structural motifs of amyloid protofilaments.
Authors: Ferguson, N. / Becker, J. / Tidow, H. / Tremmel, S. / Sharpe, T.D. / Krause, G. / Flinders, J. / Petrovich, M. / Berriman, J. / Oschkinat, H. / Fersht, A.R.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...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
Revision 1.4Dec 27, 2023Group: 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: Transcription elongation regulator 1
B: Transcription elongation regulator 1
C: Transcription elongation regulator 1
D: Transcription elongation regulator 1


Theoretical massNumber of molelcules
Total (without water)18,4964
Polymers18,4964
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)10 / 30structures 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: 4624.035 Da / Num. of mol.: 4 / Fragment: second WW domain / Mutation: Y446F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCERG1, CA150, TAF2S / Plasmid: pGAT2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14776

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111MAS CP-PDSD
221MAS CP-PDSD
331MAS CP-PDSD
441MAS CP-PDSD
NMR detailsText: 4mm and 3.2mm triple resonance MAS probes were used and spinning of 10.5 kHz was applied.

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Sample preparation

Details
Solution-IDContentsSolvent system
1uniform 13C,15N labeling, 15 mg fibre in phosphate bufferphosphate buffer
2uniform 2H,13C,15N labeling, 15 mg fibre in phosphate bufferphosphate buffer
3uniform 15N labeling, 13C labeling is based on 1,3[13C]-glycerol as carbon source for the bacteria, 15 mg fibre in phosphate bufferphosphate buffer
4uniform 15N labeling, 13C labeling is based on 2[13C]-glycerol as carbon source for the bacteria, 15 mg fibre in phosphate bufferphosphate buffer
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 285 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Brukercollection
Sparky3.1Goddard, T.D., Kneller, D.G.data analysis
Amber7Case, D.A. et al.structure solution
Amber7Case, D.A. et al.refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: simulated annealing was performed with 25 MAS-NMR derived long range distance constraints and hydrogend bond constraints between the beta strands of 6 repeat units of the protofilament. ...Details: simulated annealing was performed with 25 MAS-NMR derived long range distance constraints and hydrogend bond constraints between the beta strands of 6 repeat units of the protofilament. Conformer (residues 0-30; 0=M of the N-terminal GSM tag) of lowest energy of the four inner repeat units was subjected to a 1 ns molecular dynamics simulation in water. To distinguish the residues per repeat unit, for annotation an initial digid as hundred is added , such as A: 200-230, B: 300-330, C: 400-430, D: 500-530)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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