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- PDB-2opu: Solution NMR Structure of the First Domain of KSRP -

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Basic information

Entry
Database: PDB / ID: 2opu
TitleSolution NMR Structure of the First Domain of KSRP
ComponentsKHSRP protein
KeywordsRNA BINDING PROTEIN / KH DOMAIN / KSRP
Function / homology
Function and homology information


positive regulation of mRNA catabolic process / negative regulation of low-density lipoprotein particle clearance / ATF4 activates genes in response to endoplasmic reticulum stress / miRNA metabolic process / 3'-UTR-mediated mRNA destabilization / negative regulation of nitric oxide biosynthetic process / mRNA 3'-UTR AU-rich region binding / RNA splicing, via transesterification reactions / KSRP (KHSRP) binds and destabilizes mRNA / regulation of alternative mRNA splicing, via spliceosome ...positive regulation of mRNA catabolic process / negative regulation of low-density lipoprotein particle clearance / ATF4 activates genes in response to endoplasmic reticulum stress / miRNA metabolic process / 3'-UTR-mediated mRNA destabilization / negative regulation of nitric oxide biosynthetic process / mRNA 3'-UTR AU-rich region binding / RNA splicing, via transesterification reactions / KSRP (KHSRP) binds and destabilizes mRNA / regulation of alternative mRNA splicing, via spliceosome / cellular response to cytokine stimulus / mRNA transport / protein folding chaperone / regulation of mRNA stability / RNA splicing / mRNA processing / regulation of gene expression / mRNA binding / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 ...: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Far upstream element-binding protein 2 / Far upstream element-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDiaz-Moreno, I. / Ramos, A. / Garcia-Mayoral, M.F. / Hollingworth, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Phosphorylation-mediated unfolding of a KH domain regulates KSRP localization via 14-3-3 binding.
Authors: Diaz-Moreno, I. / Hollingworth, D. / Frenkiel, T.A. / Kelly, G. / Martin, S. / Howell, S. / Garcia-Mayoral, M. / Gherzi, R. / Briata, P. / Ramos, A.
History
DepositionJan 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Dec 27, 2023Group: 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: KHSRP protein


Theoretical massNumber of molelcules
Total (without water)9,4121
Polymers9,4121
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)25 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein KHSRP protein / KH1 DOMAIN OF K-HOMOLOGY SPLICING RECOGNITION PROTEIN


Mass: 9411.697 Da / Num. of mol.: 1 / Fragment: KH DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHSRP / Plasmid: pGEX-JDK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5U4P6, UniProt: Q92945*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D HNCA
1313D HNCO
1413D 13C-NOESY-HSQC
1523D 15N-NOESY-HSQC
162HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM KH1 U-15N,13C; 10mM Tris-HCl pH 7.4; 100mM NaCl; 1mM TCEP; 90% H2O, 10% D2O90% H2O/10% D2O
21mM KH1 U-15N; 10mM Tris-HCl pH 7.4; 100mM NaCl; 1mM TCEP; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.4 / Pressure: ambient / Temperature: 300 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR1.1Hallcollection
NMRPipe2.5Delaglioprocessing
XEASY2Bartelsdata analysis
Sparky3.11Goddarddata analysis
ARIA1.2Lingestructure solution
ARIA1.2Lingerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1908 restraints, 1822 are NOE-derived distance constraints, 57 dihedral angle restraints, 29 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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