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- PDB-2ymj: Solution structure of the QUA1 dimerization domain of pXqua, the ... -

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Basic information

Entry
Database: PDB / ID: 2ymj
TitleSolution structure of the QUA1 dimerization domain of pXqua, the Xenopus ortholog of Quaking.
ComponentsPROTEIN QUAKING-A
KeywordsTRANSLATION / HAIRPIN / QKI / STAR PROTEIN
Function / homology
Function and homology information


notochord cell differentiation / spliceosome-depend formation of circular RNA / regulation of astrocyte differentiation / negative regulation of macrophage differentiation / notochord formation / notochord development / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / mRNA transport / regulation of translation ...notochord cell differentiation / spliceosome-depend formation of circular RNA / regulation of astrocyte differentiation / negative regulation of macrophage differentiation / notochord formation / notochord development / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / mRNA transport / regulation of translation / single-stranded RNA binding / mRNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4010 / Protein quaking, putative nuclear localisation signal / Putative nuclear localisation signal of quaking / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / K Homology domain, type 1 superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4010 / Protein quaking, putative nuclear localisation signal / Putative nuclear localisation signal of quaking / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / K Homology domain, type 1 superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / K Homology domain / K homology RNA-binding domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
KH domain-containing RNA-binding protein qki.S
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodSOLUTION NMR / ARIA VERSION 2.3
AuthorsAli, M. / Broadhurst, R.W.
CitationJournal: Plos One / Year: 2013
Title: Solution Structure of the Qua1 Dimerization Domain of Pxqua, the Xenopus Ortholog of Quaking.
Authors: Ali, M. / Broadhurst, R.W.
History
DepositionOct 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary
Revision 1.2Sep 25, 2019Group: 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 1.3Jun 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 1.4Jul 3, 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

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Assembly

Deposited unit
A: PROTEIN QUAKING-A
B: PROTEIN QUAKING-A


Theoretical massNumber of molelcules
Total (without water)12,2782
Polymers12,2782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LOWEST ENERGY PLUS NO NOE VIOLATIONS >0.5 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS > 5 DEGREES
RepresentativeModel #1

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Components

#1: Protein PROTEIN QUAKING-A / PXQUA / XQUA


Mass: 6139.150 Da / Num. of mol.: 2 / Fragment: QUA1 DOMAIN, RESIDUES 8-57 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CONTAINS AN EXTRA GS CLONING ARTEFACT AT THE N-TERMINUS
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Plasmid: PMAT10-QUA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q32NN2
Sequence detailsCONSTRUCT CORRESPONDS TO RESIDUES 32 TO 81 OF PXQUA, WITH AN ADDITION GS CLONING ARTEFACT AT THE N- ...CONSTRUCT CORRESPONDS TO RESIDUES 32 TO 81 OF PXQUA, WITH AN ADDITION GS CLONING ARTEFACT AT THE N-TERMINUS, PLUS A C59S POINT MUTATION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111[1H
12115N]-HSQC
13115N-TOCSY- HSQC
14115N-NOESY-HSQC
15113C- NOESY-HSQC
161HNCA
171HN(CO)CA
181HN(CA)CB
191CBCA(CO)NH
1101HNCO
1111HBHA(CO)NH
1121(H)CCH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON A UNIFORMLY 15N AND 13C LABELLED PXQUA QUA1 DOMAIN SAMPLE.

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Sample preparation

DetailsContents: 90% WATER / 10% D2O
Sample conditionsIonic strength: 150 mM / pH: 6 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA/CNSNILGES ET ALrefinement
CcpNmr AnalysisANALYSISstructure solution
RefinementMethod: ARIA VERSION 2.3 / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY PLUS NO NOE VIOLATIONS >0.5 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS > 5 DEGREES
Conformers calculated total number: 40 / Conformers submitted total number: 20

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