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- PDB-1h95: Solution structure of the single-stranded DNA-binding Cold Shock ... -

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Entry
Database: PDB / ID: 1h95
TitleSolution structure of the single-stranded DNA-binding Cold Shock Domain (CSD) of human Y-box protein 1 (YB1) determined by NMR (10 lowest energy structures)
ComponentsY-BOX BINDING PROTEIN
KeywordsTRANSLATION FACTOR / TRANSCRIPTION FACTOR / OB-FOLD / 5-STRANDED ANTI-PARALLEL BETA-BARREL / SINGLE STRANDED DNA BINDING / COLD SHOCK / Y-BOX
Function / homology
Function and homology information


tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Noncanonical activation of NOTCH3 / RNA transport / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule ...tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Noncanonical activation of NOTCH3 / RNA transport / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / histone pre-mRNA 3'end processing complex / embryonic morphogenesis / U12-type spliceosomal complex / positive regulation of cytoplasmic translation / mRNA stabilization / cellular response to interleukin-7 / miRNA binding / mRNA Splicing - Minor Pathway / negative regulation of cellular senescence / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of cell division / epidermis development / mRNA Splicing - Major Pathway / RNA splicing / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / P-body / mRNA processing / cytoplasmic stress granule / Interferon gamma signaling / sequence-specific double-stranded DNA binding / GTPase binding / single-stranded DNA binding / regulation of gene expression / double-stranded DNA binding / in utero embryonic development / nucleic acid binding / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / mRNA binding / chromatin binding / synapse / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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) ...: / 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
Y-box-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED MD
AuthorsKloks, C.P.A.M. / Spronk, C.A.E.M. / Hoffmann, A. / Vuister, G.W. / Grzesiek, S. / Hilbers, C.W.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Solution Structure and DNA-Binding Properties of the Cold-Shock Domain of the Human Y-Box Protein Yb-1.
Authors: Kloks, C.P.A.M. / Spronk, C.A.E.M. / Lasonder, E. / Hoffmann, A. / Vuister, G.W. / Grzesiek, S. / Hilbers, C.W.
History
DepositionFeb 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2002Provider: repository / Type: Initial release
Revision 1.1May 7, 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 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Y-BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)8,7551
Polymers8,7551
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)10 / 10
RepresentativeModel #1

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Components

#1: Protein Y-BOX BINDING PROTEIN / CSD


Mass: 8754.899 Da / Num. of mol.: 1 / Fragment: COLD SHOCK DOMAIN
Source method: isolated from a genetically manipulated source
Details: SINGLE STRANDED DNA BINDING COLD SHOCK DOMAIN(CSD) OF HUMAN Y-BOX PROTEIN 1 (YB-1)
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P67809*PLUS
Sequence detailsTHE SEQUENCE IS MATCHES TO SWISS PROT ENTRY Q90376 (RESIDUES 15-92) WHICH REPRESENTS Y-BOX BINDING ...THE SEQUENCE IS MATCHES TO SWISS PROT ENTRY Q90376 (RESIDUES 15-92) WHICH REPRESENTS Y-BOX BINDING PROTEIN FROM COLUMBA LIVIA (DOMESTIC PIGEON). N-TERMINAL METHIONINE ADDED IN PDB-SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED NOESY
12115N-EDITED ROESY
13113C-EDITED NOESY
141HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N AND 15N/13C LABELLED COLD SHOCK DOMAIN OF HUMAN YB-1

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Sample preparation

Sample conditionsIonic strength: 0 / pH: 6.7 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORX-PLORNILGESrefinement
NMRPipestructure solution
PIPPstructure solution
X-PLORstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, RESTRAINED MD / Software ordinal: 1 / Details: RESTRAINED MD
NMR ensembleConformers calculated total number: 10 / Conformers submitted total number: 10

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