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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND CUT DOMAIN OF HUMAN SATB2
 
Authors :  K. Inoue, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  21 May 05  (Deposition) - 21 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cut Domain, Dna-Binding Protein Satb2, Special At-Rich Sequence-Binding Protein 2, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Inoue, F. Hayashi, S. Yokoyama
Solution Structure Of The Second Cut Domain Of Human Satb2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN SATB2
    ChainsA
    EngineeredYES
    Expression System PlasmidP040705-12
    Expression System Vector TypePLASMID
    FragmentCUT DOMAIN
    GeneKAZUSA CDNA FH00753
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymSPECIAL AT-RICH SEQUENCE-BINDING PROTEIN 2

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CSF)

(-) Sites  (0, 0)

(no "Site" information available for 2CSF)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CSF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CSF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CSF)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUTPS51042 CUT domain profile.SATB2_HUMAN350-437
473-560
  1-
A:8-95

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002609262bENSE00001551754chr2:200329831-200329559273SATB2_HUMAN-00--
1.3ENST000002609263ENSE00001402939chr2:200325255-20032517581SATB2_HUMAN-00--
1.5bENST000002609265bENSE00002187581chr2:200320819-200320592228SATB2_HUMAN1-57570--
1.6aENST000002609266aENSE00000964856chr2:200298237-200298061177SATB2_HUMAN57-116600--
1.10ENST0000026092610ENSE00000964857chr2:200246543-200246417127SATB2_HUMAN116-158430--
1.11ENST0000026092611ENSE00000934554chr2:200245210-200245087124SATB2_HUMAN158-199420--
1.12dENST0000026092612dENSE00000934553chr2:200233430-200233328103SATB2_HUMAN200-234350--
1.13aENST0000026092613aENSE00000934548chr2:200213896-200213424473SATB2_HUMAN234-3911580--
1.14cENST0000026092614cENSE00000934547chr2:200193633-200193421213SATB2_HUMAN392-462711A:1-77
1.17ENST0000026092617ENSE00000934544chr2:200188681-200188526156SATB2_HUMAN463-514521A:8-4942
1.18bENST0000026092618bENSE00000934543chr2:200173680-200173483198SATB2_HUMAN515-580661A:50-9546
1.19cENST0000026092619cENSE00001156800chr2:200137395-2001342313165SATB2_HUMAN581-7331531A:96-101 (gaps)8

(-) 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:101
 aligned with SATB2_HUMAN | Q9UPW6 from UniProtKB/Swiss-Prot  Length:733

    Alignment length:143
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591   
          SATB2_HUMAN   452 SSSPSSSRTPQAKTSTPTTDLPIKVDGANINITAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQHERDVIYEEESRHHHSERMQHVVQLPPEPVQVLHRQQSQPAKESS 594
               SCOP domains ---------------------d2csfa1 A:8-95 DNA-binding protein SATB2                                                ---------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......--------------............hhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh--------------------------....--.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------CUT  PDB: A:8-95 UniProt: 473-560                                                       ---------------------------------- PROSITE
               Transcript 1 Exon 1.14c Exon 1.17  PDB: A:8-49 UniProt: 463-514 [INCOMPLETE]Exon 1.18b  PDB: A:50-95 UniProt: 515-580 [INCOMPLETE]            Exon 1.19c     Transcript 1
                 2csf A   1 GSSGSSG--------------PIKVDGANINITAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQHERDVIYEEES--------------------------SGPS--SG 101
                                  |  -         - |      16        26        36        46        56        66        76        86        |-         -         -     |  |- | 
                                  7              8                                                                                     95                         96 99  | 
                                                                                                                                                                       100 

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CSF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CSF)

(-) Gene Ontology  (26, 26)

NMR Structure(hide GO term definitions)
Chain A   (SATB2_HUMAN | Q9UPW6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    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:0071310    cellular response to organic substance    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 an organic substance stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0021902    commitment of neuronal cell to specific neuron type in forebrain    The commitment of neuronal precursor cells to become specialized types of neurons in the forebrain.
    GO:0009880    embryonic pattern specification    The process that results in the patterns of cell differentiation that will arise in an embryo.
    GO:0048704    embryonic skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    GO:0002076    osteoblast development    The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    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:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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