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- PDB-2jvz: Solution NMR Structure of the Second and Third KH Domains of KSRP -

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Basic information

Entry
Database: PDB / ID: 2jvz
TitleSolution NMR Structure of the Second and Third KH Domains of KSRP
ComponentsFar upstream element-binding protein 2
KeywordsSPLICING / RNA Binding Protein / KH Domain / KSRP / Posttranscriptional Regulation / mRNA decay
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDiaz-Moreno, I. / Hollingworth, D. / Garcia-Mayoral, M.F. / Kelly, G. / Cukier, C.D. / Ramos, A.
Citation
Journal: To be Published / Year: 2007
Title: Solution NMR Structure of the Second and Third KH Domains of KSRP
Authors: Diaz-Moreno, I. / Hollingworth, D. / Garcia-Mayoral, M.F. / Kelly, G. / Martin, S. / Chen, C.Y. / Ramos, A.
#1: Journal: Structure / Year: 2007
Title: The Structure of the C-Terminal Domains of KSRP Reveals an Element Important to mRNA Degradation
Authors: Garcia-Mayoral, M.F. / Hollingworth, D. / Masino, L. / Diaz-Moreno, I. / Kelly, G. / Gherzi, R.R. / Chou, C.F. / Chen, C.Y. / Ramos, A.
History
DepositionSep 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Far upstream element-binding protein 2


Theoretical massNumber of molelcules
Total (without water)17,7621
Polymers17,7621
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 Far upstream element-binding protein 2 / FUSE-binding protein 2 / KH type-splicing regulatory protein / KSRP / p75


Mass: 17762.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHSRP, FUBP2 / Plasmid details: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q92945

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1323D HN(CA)CB
1423D HNCA
1523D HNCO
1613D HNHA
1723D CBCA(CO)NH
1823D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.8 mM [U-100% 15N] entity_2, 10 mM TRIS, 50 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.8 mM [U-100% 13C; U-100% 15N] entity_2, 10 mM TRIS, 50 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMentity_1[U-100% 15N]1
10 mMTRIS1
50 mMsodium chloride1
1 mMTCEP1
0.4 mMentity_1[U-100% 13C; U-100% 15N]2
10 mMTRIS2
50 mMsodium chloride2
1 mMTCEP2
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
VNMRv 1.1Variancollection
TopSpinv. 2.0Bruker Biospincollection
NMRPipev 2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipev 2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
SparkyV 3.11Goddardchemical shift assignment
XEASYBartels et al.chemical shift assignment
ARIAv 1.2Linge, O'Donoghue and Nilgesstructure solution
ARIAv 1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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