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Yorodumi- PDB-1h95: Solution structure of the single-stranded DNA-binding Cold Shock ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h95 | ||||||
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Title | Solution 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) | ||||||
Components | Y-BOX BINDING PROTEIN | ||||||
Keywords | TRANSLATION 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 / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / CRD-mediated mRNA stabilization ...tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / 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 / P-body / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / cytoplasmic stress granule / Interferon gamma signaling / sequence-specific double-stranded DNA binding / single-stranded DNA binding / GTPase binding / double-stranded DNA binding / regulation of gene expression / in utero embryonic development / negative regulation of translation / nucleic acid binding / ribonucleoprotein complex / mRNA binding / intracellular membrane-bounded organelle / synapse / chromatin binding / 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 | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED MD | ||||||
Authors | Kloks, C.P.A.M. / Spronk, C.A.E.M. / Hoffmann, A. / Vuister, G.W. / Grzesiek, S. / Hilbers, C.W. | ||||||
Citation | Journal: 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 |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h95.cif.gz | 242.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h95.ent.gz | 203.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/1h95 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/1h95 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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Sequence details | THE 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N AND 15N/13C LABELLED COLD SHOCK DOMAIN OF HUMAN YB-1 |
-Sample preparation
Sample conditions | Ionic strength: 0 / pH: 6.7 / Pressure: 1 atm / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS, RESTRAINED MD / Software ordinal: 1 / Details: RESTRAINED MD | ||||||||||||||||||||
NMR ensemble | Conformers calculated total number: 10 / Conformers submitted total number: 10 |