1H95 Translation Factor date Feb 23, 2001
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)
authors C.P.A.M.Kloks, C.A.E.M.Spronk, A.Hoffmann, G.W.Vuister, S.Grzesiek, C.W.Hilbers
compound source
Molecule: Y-Box Binding Protein
Chain: A
Fragment: Cold Shock Domain
Synonym: Csd
Engineered: Yes
Other_details: Single Stranded Dna Binding Cold Shock Domain(Csd) Of Human Y-Box Protein 1 (Yb-1)
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet11a
methodSolution NMR
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1., Kloks CP, Spronk CA, Lasonder E, Hoffmann A, Vuister GW, Grzesiek S, Hilbers CW, J Mol Biol 2002 Feb 15;316(2):317-26. PMID:11851341
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (203 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1H95
  • Original NMR restraints for 1H95 from PDB
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1H95 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1H95 from S2C, [Save to disk]
    • View 1H95 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1H95
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1H95, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1h95a_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1h95_A] [1h95]
  • SWISS-PROT database: [P67809]
  • Domain organization of [YBOX1_HUMAN] by SWISSPFAM
  • Domain found in 1H95: [CSP ] by SMART
    • Other resources with information on 1H95
  • Community annotation for 1H95 at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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