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- PDB-2yty: Solution structure of the fourth cold-shock domain of the human K... -

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Basic information

Entry
Database: PDB / ID: 2yty
TitleSolution structure of the fourth cold-shock domain of the human KIAA0885 protein (UNR protein)
ComponentsCold shock domain-containing protein E1
KeywordsRNA BINDING PROTEIN / CELL-FREE PROTEIN SYNTHESIS / BETA-BARREL / TRANSLATIONAL REGULATION / RNA CHAPERONE / RNA/DNA BINDING / QB FOLD / GREEK-KEY TOPOLOGY / UNR PROTEIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


CRD-mediated mRNA stability complex / mCRD-mediated mRNA stability complex / nuclear-transcribed mRNA catabolic process, no-go decay / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RISC complex binding / CRD-mediated mRNA stabilization / IRES-dependent viral translational initiation / positive regulation of cytoplasmic translation / regulation of translational initiation / lncRNA binding ...CRD-mediated mRNA stability complex / mCRD-mediated mRNA stability complex / nuclear-transcribed mRNA catabolic process, no-go decay / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RISC complex binding / CRD-mediated mRNA stabilization / IRES-dependent viral translational initiation / positive regulation of cytoplasmic translation / regulation of translational initiation / lncRNA binding / stress granule assembly / positive regulation of translation / P-body / RNA stem-loop binding / male gonad development / cytoplasmic stress granule / mRNA binding / Golgi apparatus / RNA binding / plasma membrane / cytosol
Similarity search - Function
SUZ-C motif / SUZ-C domain / SUZ-C domain profile. / : / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. ...SUZ-C motif / SUZ-C domain / SUZ-C domain profile. / : / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cold shock domain-containing protein E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Struct.Funct.Genom. / Year: 2010
Title: The NMR solution structures of the five constituent cold-shock domains (CSD) of the human UNR (upstream of N-ras) protein.
Authors: Goroncy, A.K. / Koshiba, S. / Tochio, N. / Tomizawa, T. / Inoue, M. / Watanabe, S. / Harada, T. / Tanaka, A. / Ohara, O. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cold shock domain-containing protein E1


Theoretical massNumber of molelcules
Total (without water)9,4221
Polymers9,4221
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Cold shock domain-containing protein E1 / UNR protein / N-ras upstream gene protein


Mass: 9422.335 Da / Num. of mol.: 1 / Fragment: FOURTH COLD-SHOCK DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: KIAA0885 / Plasmid: P040114-51 / References: UniProt: O75534

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.09mM COLD-SHOCK DOMAIN, 20mM PHOSPHATE BUFFER NA, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 mM / pH: 6 / Pressure: AMBIENT / Temperature: 296 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.2P.GUNTERT ET AL.refinement
CYANA2.2.2P.GUNTERT ET AL.structure solution
XwinNMR3.5BRUKERcollection
NMRPipe20060702FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.9821NAOHIRO KOBAYASHIdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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