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- PDB-2bl5: Solution structure of the KH-QUA2 region of the Xenopus STAR-GSG ... -

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Basic information

Entry
Database: PDB / ID: 2bl5
TitleSolution structure of the KH-QUA2 region of the Xenopus STAR-GSG Quaking protein.
ComponentsMGC83862 PROTEIN
KeywordsRNA BINDING / STAR PROTEINS / GSG PROTEINS / QUAKING
Function / homology
Function and homology information


notochord cell differentiation / regulation of astrocyte differentiation / negative regulation of macrophage differentiation / notochord formation / notochord development / multicellular organism development / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / mRNA transport / RNA splicing ...notochord cell differentiation / regulation of astrocyte differentiation / negative regulation of macrophage differentiation / notochord formation / notochord development / multicellular organism development / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / mRNA transport / RNA splicing / mRNA processing / regulation of translation / single-stranded RNA binding / cell differentiation / mRNA binding / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein quaking, putative nuclear localisation signal / Putative nuclear localisation signal of quaking / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily ...Protein quaking, putative nuclear localisation signal / Putative nuclear localisation signal of quaking / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
KH domain-containing RNA-binding protein qki.S / Protein quaking-B
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodSOLUTION NMR / ARIA
AuthorsMaguire, M.L. / Guler-Gane, G. / Nietlispach, D. / Raine, A.R.C. / Zorn, A.M. / Standart, N. / Broadhurst, R.W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Solution Structure and Backbone Dynamics of the Kh-Qua2 Region of the Xenopus Star/Gsg Quaking Protein
Authors: Maguire, M.L. / Guler-Gane, G. / Nietlispach, D. / Raine, A.R.C. / Zorn, A.M. / Standart, N. / Broadhurst, R.W.
History
DepositionMar 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MGC83862 PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,0961
Polymers16,0961
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)17 / 50NO DISTANCE RESTRAINT VIOLATIONS GREATER THAN 0.5 ANGSTROMS AND NO DIHEDRAL ANGLE RESTRAINT VIOLATIONS GREATER THAN 5 DEGREES
RepresentativeModel #1

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Components

#1: Protein MGC83862 PROTEIN / QUAKING PROTEIN


Mass: 16095.632 Da / Num. of mol.: 1 / Fragment: KH-QUA2 REGION, RESIDUES 82-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog)
Description: GENE EXPRESSION WAS INDUCED BY THE ADDITION OF IPTG TO A FINAL CONCENTRATION OF 0.5 MM AND THE CELLS WERE INCUBATED FOR 3 H AT 37 DEGREES C. THE CELLS WERE HARVESTED BY CENTRIFUGATION AT ...Description: GENE EXPRESSION WAS INDUCED BY THE ADDITION OF IPTG TO A FINAL CONCENTRATION OF 0.5 MM AND THE CELLS WERE INCUBATED FOR 3 H AT 37 DEGREES C. THE CELLS WERE HARVESTED BY CENTRIFUGATION AT 6000 RPM FOR 20 MIN AND STORED AT -20 DEGREES C UNTIL REQUIRED. THE CELLS WERE RESUSPENDED IN TE BUFFER (CONTAINING 1 MM EDTA, 25 MM TRIS) AT PH 8.0 AND THEN BROKEN IN A FRENCH PRESS. THE CELL DEBRIS WAS REMOVED BY CENTRIFUGATION AT 40000 G FOR 30 MIN, FOLLOWING WHICH THE PELLET WAS RESUSPENDED IN 50 ML OF 20 MM SODIUM PHOSPHATE CONTAINING 10 PER CENT TRITON X-100 AND 100 MM SODIUM CHLORIDE. THE CRUDE EXTRACT WAS ADDED TO 6 ML OF NI-NTA RESIN (QIAGEN), MIXED FOR 2 H AT 4 DEGREES C, SPUN DOWN AT 5000 G FOR 10 MIN AND THE SUPERNATANT DISCARDED. THE BEADS WERE LOADED ON TO A COLUMN, WASHED WITH 2 VOLUMES OF RESUSPENSION BUFFER AND THEN 2 VOLUMES OF ELUTION BUFFER (CONTAINING 500 MM IMIDAZOLE, 50 MM SODIUM CHLORIDE AND 20 MM SODIUM PHOSPHATE). THE ELUATE WAS DESALTED ON A SEPHADEX G-25 PD-10 COLUMN (PHARMACIA) AND THEN CONCENTRATED TO 1 MM USING A BIOMAX 10K MEMBRANE TO A FINAL VOLUME OF 500 MICROLITRES. THE PROTEIN PRODUCT CORRESPONDS TO RESIDUES 81 TO 214 OF FULL LENGTH PXQUA, WITH A C-TERMINAL HIS6 EXTENSION
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IRN2, UniProt: Q32NN2*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-TOCSY-HSQC
12115N-NOESY- HSQC
131HN(CA)CB
141CBCA(CO)NH
151HNCO
161(H)CCH-TOCSY
17113C- NOESY-HSQCHCCH-TOCSY
18113C- NOESY-HSQC
NMR detailsText: STRUCTURE WAS DETERMINED USING A 13C,15N-LABELLED PROTEIN SAMPLE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2LINGE,HABECK,REIPING,NILGESrefinement
ANSIGstructure solution
RefinementMethod: ARIA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: NO DISTANCE RESTRAINT VIOLATIONS GREATER THAN 0.5 ANGSTROMS AND NO DIHEDRAL ANGLE RESTRAINT VIOLATIONS GREATER THAN 5 DEGREES
Conformers calculated total number: 50 / Conformers submitted total number: 17

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