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(-) Description

Title :  SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE
 
Authors :  P. D. Cary, C. M. Read, B. Davis, P. C. Driscoll, C. Crane-Robinson
Date :  30 Jan 01  (Deposition) - 14 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Hmg Box, Dna Bending, Dna Recognition, Chromatin, Nmr, Dna Binding Protein, Dna Sequence Specific, Testis Determining. (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. D. Cary, C. M. Read, B. Davis, P. C. Driscoll, C. Crane-Robinson
Solution Structure And Backbone Dynamics Of The Dna-Binding Domain Of Mouse Sox-5.
Protein Sci. V. 10 83 2001
PubMed-ID: 11266597  |  Reference-DOI: 10.1110/PS.32801
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR SOX-5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21 (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHMG BOX
    GeneSOX-5
    OrganTESTIS
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  
NMR Structure (30x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1I11)

(-) Sites  (0, 0)

(no "Site" information available for 1I11)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I11)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I11)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I11)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.SOX5_MOUSE556-624  1A:3-70

(-) Exons   (0, 0)

(no "Exon" information available for 1I11)

(-) 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:70
 aligned with SOX5_MOUSE | P35710 from UniProtKB/Swiss-Prot  Length:763

    Alignment length:70
                                   563       573       583       593       603       613       623
           SOX5_MOUSE   554 PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY 623
               SCOP domains d1i11a_ A: Sox-5                                                       SCOP domains
               CATH domains 1i11A00 A:1-70 DNA Binding (I), subunit A                              CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HMG_BOX_2  PDB: A:3-70 UniProt: 556-624                              PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 1i11 A   1 PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY  70
                                    10        20        30        40        50        60        70

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I11)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (SOX5_MOUSE | P35710)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0055059    asymmetric neuroblast division    The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0071560    cellular response to transforming growth factor beta stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
    GO:0021953    central nervous system neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048709    oligodendrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
    GO:0061036    positive regulation of cartilage development    Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0032332    positive regulation of chondrocyte differentiation    Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
    GO:2000741    positive regulation of mesenchymal stem cell differentiation    Any process that activates or increases the frequency, rate or extent of mesenchymal stem cell differentiation.
    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:0060164    regulation of timing of neuron differentiation    The process controlling the activation and/or rate at which a relatively unspecialized cell acquires features of a neuron.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0044798    nuclear transcription factor complex    A protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
    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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