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- PDB-2elj: Solution structure of the SWIRM domain of baker's yeast Transcrip... -

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Basic information

Entry
Database: PDB / ID: 2elj
TitleSolution structure of the SWIRM domain of baker's yeast Transcriptional adapter 2
ComponentsTranscriptional adapter 2
KeywordsTRANSCRIPTION / YDR448W / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ADA complex / : / SAGA-type complex / replication-born double-strand break repair via sister chromatid exchange / SLIK (SAGA-like) complex / rDNA heterochromatin formation / SAGA complex / phosphatidylserine binding / subtelomeric heterochromatin formation / chromatin organization ...ADA complex / : / SAGA-type complex / replication-born double-strand break repair via sister chromatid exchange / SLIK (SAGA-like) complex / rDNA heterochromatin formation / SAGA complex / phosphatidylserine binding / subtelomeric heterochromatin formation / chromatin organization / chromosome, telomeric region / transcription coactivator activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type ...Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional adapter 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYoneyama, M. / Tochio, N. / Koshiba, S. / Tomizawa, T. / Watanabe, S. / Harada, T. / Umehara, T. / Tanaka, A. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SWIRM domain of baker's yeast Transcriptional adapter 2
Authors: Yoneyama, M. / Tochio, N. / Koshiba, S. / Tomizawa, T. / Watanabe, S. / Harada, T. / Umehara, T. / Tanaka, A. / Kigawa, T. / Yokoyama, S.
History
DepositionMar 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.3May 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: Transcriptional adapter 2


Theoretical massNumber of molelcules
Total (without water)9,9571
Polymers9,9571
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 / 100structures with the least restraint violations,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional adapter 2


Mass: 9957.425 Da / Num. of mol.: 1 / Fragment: SWIRM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: cell-free protein synthesis / Gene: ADA2 / Plasmid: P060216-01 / References: UniProt: Q02336

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.3mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE2 / Manufacturer: Bruker / Model: AVANCE2 / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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