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- PDB-2hh3: Solution structure of the third KH domain of KSRP -

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Basic information

Entry
Database: PDB / ID: 2hh3
TitleSolution structure of the third KH domain of KSRP
ComponentsKH-type splicing regulatory protein
KeywordsRNA BINDING PROTEIN / KH-RNA binding domain
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 / torsion angle dynamics
AuthorsGarcia-Mayoral, M.F.
CitationJournal: Structure / Year: 2007
Title: The Structure of the C-Terminal KH Domains of KSRP Reveals a Noncanonical Motif Important for mRNA Degradation.
Authors: Garcia-Mayoral, M.F. / Hollingworth, D. / Masino, L. / Diaz-Moreno, I. / Kelly, G. / Gherzi, R. / Chou, C.F. / Chen, C.Y. / Ramos, A.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: KH-type splicing regulatory protein


Theoretical massNumber of molelcules
Total (without water)10,8501
Polymers10,8501
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein KH-type splicing regulatory protein


Mass: 10850.398 Da / Num. of mol.: 1 / Fragment: Third KH domain (Residues 142-212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59EZ9, UniProt: Q92945*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM KSRP 15N-KH3, 10 mM Tris, 100 mM NaCl, 1mM TCEP90% H2O/10% D2O
20.5 mM KSRP 15N,13C-KH3, 10 mM Tris, 100 mM NaCl, 1mM TCEP90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 7.4 / Pressure: ambient / Temperature: 288 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 INOVAVarianINOVA8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR3.5collection
VNMRcollection
NMRPipeF. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, A. Baxprocessing
SparkyT.D. Goddard, D.G. Knellerdata analysis
ARIA1.2J. Linge, S. O'Donoghue, M. Nilgesstructure solution
ARIA1.2J. Linge, S. O'Donoghue, M. Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Refinement in water solvent
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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