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(-) Description

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
Date :  23 Feb 01  (Deposition) - 21 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Translation Factor, Transcription Factor, Ob-Fold, 5- Stranded Anti-Parallel Beta-Barrel, Single Stranded Dna Binding, Cold Shock, Y-Box (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. P. A. M. Kloks, C. A. E. M. Spronk, E. Lasonder, A. Hoffmann, G. W. Vuister, S. Grzesiek, C. W. Hilbers
The Solution Structure And Dna-Binding Properties Of The Cold-Shock Domain Of The Human Y-Box Protein Yb-1.
J. Mol. Biol. V. 316 317 2002
PubMed-ID: 11851341  |  Reference-DOI: 10.1006/JMBI.2001.5334

(-) Compounds

Molecule 1 - Y-BOX BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: COLD SHOCK DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SINGLE STRANDED DNA BINDING COLD SHOCK DOMAIN(CSD) OF HUMAN Y-BOX PROTEIN 1 (YB-1)
    Synonym: CSD

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1H95)

(-) Sites  (0, 0)

(no "Site" information available for 1H95)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H95)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H95)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H95)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COLD_SHOCKPS00352 'Cold-shock' domain signature.YBOX1_HUMAN72-91  1A:22-41

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003213581aENSE00001458061chr1:43148098-43148402305YBOX1_HUMAN1-56561A:1-66
1.2cENST000003213582cENSE00001080452chr1:43149074-4314913764YBOX1_HUMAN56-77221A:6-2722
1.3ENST000003213583ENSE00001777538chr1:43159161-4315919434YBOX1_HUMAN77-88121A:27-3812
1.4ENST000003213584ENSE00001596728chr1:43161870-4316195990YBOX1_HUMAN89-118301A:39-6830
1.5bENST000003213585bENSE00001285477chr1:43162313-43162615303YBOX1_HUMAN119-2191011A:69-7911
1.6cENST000003213586cENSE00002149556chr1:43162851-4316293383YBOX1_HUMAN220-247280--
1.7bENST000003213587bENSE00001293985chr1:43166452-43166717266YBOX1_HUMAN247-324780--
1.8ENST000003213588ENSE00001681385chr1:43167652-43168020369YBOX1_HUMAN-00--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:79
 aligned with YBOX1_HUMAN | P67809 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:79
                                    60        70        80        90       100       110       120         
          YBOX1_HUMAN    51 DKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG 129
               SCOP domains d1h95a_ A: Y-box protein 1 cold shock domain (YB1-CSD)                          SCOP domains
               CATH domains 1h95A00 A:1-79 Nucleic acid-binding proteins                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeee..eeeeeeee..eeeeeee...................eeeeeeeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------COLD_SHOCK          -------------------------------------- PROSITE
           Transcript 1 (1) 1.1a  --------------------Exon 1.3    Exon 1.4  PDB: A:39-68        Exon 1.5b   Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.2c  PDB: A:6-27---------------------------------------------------- Transcript 1 (2)
                 1h95 A   1 MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG  79
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H95)

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (YBOX1_HUMAN | P67809)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0051020    GTPase binding    Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0070934    CRD-mediated mRNA stabilization    An mRNA stabilization process in which one or more RNA-binding proteins associate with a sequence in the open reading frame called the coding region instability determinant (CRD).
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:1903608    protein localization to cytoplasmic stress granule    A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0070937    CRD-mediated mRNA stability complex    A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, it may consist of IGF2BP1, HNRNPU, SYNCRIP/HNRNPQ, YBX1, and DHX9.
    GO:0005689    U12-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0071204    histone pre-mRNA 3'end processing complex    A ribonucleoprotein that binds to specific sites in, and is required for cleavage of, the 3'-end of histone pre-mRNAs. The complex contains the U7 snRNP and additional proteins, including the stem-loop binding protein (SLBP) and the exonuclease 3'hExo/Eri-1.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  1h95
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