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- PDB-2aqe: Structural and functional analysis of ada2 alpha swirm domain -

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Basic information

Entry
Database: PDB / ID: 2aqe
TitleStructural and functional analysis of ada2 alpha swirm domain
ComponentsTranscriptional adaptor 2, Ada2 alpha
KeywordsTRANSCRIPTION / helix-turn-helix
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / SAGA-type complex / : / ATAC complex / SAGA complex / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / regulation of protein phosphorylation / regulation of protein stability ...Formation of WDR5-containing histone-modifying complexes / SAGA-type complex / : / ATAC complex / SAGA complex / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / regulation of protein phosphorylation / regulation of protein stability / mitotic spindle / mitotic cell cycle / chromatin organization / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / 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 / Myb domain / Myb-like DNA-binding domain / 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 / Myb domain / Myb-like DNA-binding domain / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / 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-alpha / Transcriptional adapter 2-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsQian, C. / Zhang, Q. / Zeng, L. / Zhou, M.-M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structure and chromosomal DNA binding of the SWIRM domain
Authors: Qian, C. / Zhang, Q. / Li, S.D. / Zeng, L. / Walsh, M.J. / Zhou, M.-M.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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 1.4May 22, 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 adaptor 2, Ada2 alpha


Theoretical massNumber of molelcules
Total (without water)10,0431
Polymers10,0431
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional adaptor 2, Ada2 alpha


Mass: 10042.671 Da / Num. of mol.: 1 / Fragment: swirm domain, residues 355-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tada21 / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8BNK0, UniProt: Q8CHV6*PLUS

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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
131HNHA
141HN(CA)CB
151HNCA
161HN(CO)CACB

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM ada2 alpha swirm domain, U-15N,13C, 50mM phosphate buffer, 100mm NaCl, pH 6.5, 90% H2O, 10% D2O90% H2O/10% D2O
21mM ada2 alpha swirm domain, U-15N, 13C, 50mM phosphate buffer, 100mm NaCl, pH 6.5, 100% D2O100% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeBax, A.data analysis
CNS1.1Brunger et alrefinement
NMRView5Johnsondata analysis
ARIA1.2Nigles, M.refinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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