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- PDB-2xa6: Structural basis for homodimerization of the Src-associated durin... -

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Basic information

Entry
Database: PDB / ID: 2xa6
TitleStructural basis for homodimerization of the Src-associated during mitosis, 68 kD protein (Sam68) Qua1 domain
ComponentsKH DOMAIN-CONTAINING\,RNA-BINDING\,SIGNAL TRANSDUCTION-ASSOCIATED PROTEIN 1
KeywordsTRANSCRIPTION / STAR PROTEINS / CD44 / CELL CYCLE
Function / homology
Function and homology information


regulation of RNA export from nucleus / Grb2-Sos complex / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / poly(A) binding / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / positive regulation of translational initiation / signaling adaptor activity / SH2 domain binding ...regulation of RNA export from nucleus / Grb2-Sos complex / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / poly(A) binding / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / positive regulation of translational initiation / signaling adaptor activity / SH2 domain binding / protein tyrosine kinase binding / mRNA processing / SH3 domain binding / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / T cell receptor signaling pathway / spermatogenesis / protein domain specific binding / negative regulation of DNA-templated transcription / mRNA binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
KH domain-containing, RNA-binding, signal transduction-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CYANA, ARIA
AuthorsMeyer, N.H. / Tripsianes, K. / Vincendeaux, M. / Madl, T. / Kateb, F. / Brack-Werner, R. / Sattler, M.
CitationJournal: J. Biol. Chem. / Year: 2010
Title: Structural basis for homodimerization of the Src-associated during mitosis, 68-kDa protein (Sam68) Qua1 domain.
Authors: Meyer, N.H. / Tripsianes, K. / Vincendeau, M. / Madl, T. / Kateb, F. / Brack-Werner, R. / Sattler, M.
History
DepositionMar 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 15, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Jun 19, 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

Downloads & links

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Assembly

Deposited unit
A: KH DOMAIN-CONTAINING\,RNA-BINDING\,SIGNAL TRANSDUCTION-ASSOCIATED PROTEIN 1
B: KH DOMAIN-CONTAINING\,RNA-BINDING\,SIGNAL TRANSDUCTION-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)9,2212
Polymers9,2212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide KH DOMAIN-CONTAINING\,RNA-BINDING\,SIGNAL TRANSDUCTION-ASSOCIATED PROTEIN 1 / SAM68 / P21 RAS GTPASE-ACTIVATING PROTEIN-ASSOCIATED P62 / GAP-ASSOCIATED TYROSINE PHOSPHOPROTEIN ...SAM68 / P21 RAS GTPASE-ACTIVATING PROTEIN-ASSOCIATED P62 / GAP-ASSOCIATED TYROSINE PHOSPHOPROTEIN P62 / SRC-ASSOCIATED IN MITOSIS 68 KDA PROTEIN / P68


Mass: 4610.261 Da / Num. of mol.: 2 / Fragment: QUA1, RESIDUES 97-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 ZZ SAM68 QUA1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q07666
Sequence detailsSEQUENCE CONTAINS ADDITIONAL AMINO ACIDS GA AT THE N- TERMINUS, WHICH ARE DERIVED FROM THE EXPRESSION VECTOR.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-
12115N-EDITED NOESY
231HNCO
241HN(CA)CB
251HN(CO)CACB
361HCC(H)-TOCSY
47114N/12C- FILTERED / 13C-
48115N- EDITED NOESY
591HNCO
5101HSQC (RDC)
NMR detailsText: NONE

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Sample preparation

Details
Solution-IDContents
190% WATER, 10% D2O
290% WATER, 10% D2O
390% WATER, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM6.5 1.0 atm298.0 K
2100 mM6.5 1.0 atm298.0 K
3100 mM6.5 1.0 atm298.0 K
4100 mM6.5 1.0 atm298.0 K
5100 mM6.5 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE7502
Bruker AVANCEBrukerAVANCE6003
Bruker AVANCEBrukerAVANCE9004
Bruker ALBrukerAL7505

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Processing

NMR software
NameDeveloperClassification
ARIAJP.LINGE,MA.WILLIAMS,CA.SPRONK,AM.BONVIN,M. NILGESrefinement
NMRPipestructure solution
Sparkystructure solution
CYANAstructure solution
ARIAstructure solution
RefinementMethod: CYANA, ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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