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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIC OCT-6 (POU3F1) POU DOMAIN BOUND TO PALINDROMIC MORE DNA
 
Authors :  R. Jauch, S. H. Choo, C. K. L. Ng, P. R. Kolatkar
Date :  28 Sep 10  (Deposition) - 20 Oct 10  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transcription-Dna Complex, Sox (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Jauch, S. H. Choo, C. K. L. Ng, P. R. Kolatkar
Crystal Structure Of The Dimeric Oct6 (Pou3F1) Pou Domain Bound To Palindromic More Dna.
Proteins V. 79 674 2011
PubMed-ID: 21117060  |  Reference-DOI: 10.1002/PROT.22916

(-) Compounds

Molecule 1 - 5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*AP)-3'
    ChainsA
    SyntheticYES
 
Molecule 2 - 5'-D(*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP)-3'
    ChainsB
    SyntheticYES
 
Molecule 3 - POU DOMAIN, CLASS 3, TRANSCRIPTION FACTOR 1
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST-HISMBP
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentRESIDUES 240-402
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymOCTAMER-BINDING TRANSCRIPTION FACTOR 6, OCTAMER-BINDING PROTEIN 6, POU DOMAIN TRANSCRIPTION FACTOR SCIP, OTF-6, OCT-6

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU C:281 , TYR C:282 , SER C:300 , PHE C:301 , LYS C:302 , LYS C:393BINDING SITE FOR RESIDUE EDO C1398
2AC2SOFTWAREDT B:211 , ARG C:264 , PHE C:269 , HOH C:2018BINDING SITE FOR RESIDUE EDO C1399
3AC3SOFTWAREDT A:206 , DG A:207 , DC B:205 , CYS C:386 , ASN C:387 , GLN C:390BINDING SITE FOR RESIDUE EDO C1400
4AC4SOFTWAREDA B:210 , ASP C:273 , HOH C:2004 , HOH C:2018BINDING SITE FOR RESIDUE EDO C1401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POU_1PS00035 POU-specific (POUs) domain signature 1.PO3F1_MOUSE263-275  1C:263-275
2POU_2PS00465 POU-specific (POUs) domain signature 2.PO3F1_MOUSE287-300  1C:287-300
3HOMEOBOX_2PS50071 'Homeobox' domain profile.PO3F1_MOUSE335-395  1C:343-395
4HOMEOBOX_1PS00027 'Homeobox' domain signature.PO3F1_MOUSE370-393  1C:370-393

(-) Exons   (0, 0)

(no "Exon" information available for 2XSD)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:DNA  Length:11
                                           
                 2xsd A 201 ATGCATGAGGA 211
                                   210 

Chain B from PDB  Type:DNA  Length:11
                                           
                 2xsd B 202 CCTCATGCATA 212
                                   211 

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with PO3F1_MOUSE | P21952 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:151
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
          PO3F1_MOUSE   247 APSSDDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP 397
               SCOP domains d2xsdc1 C:247-319 automated matches                                      -----------------------d2xsdc2 C:343-397 automated matches                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Pou-2xsdC02 C:247-319                                                    -----------------------Homeobox-2xsdC01 C:343-394                          --- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh-----------------------..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------POU_1        -----------POU_2         ----------------------------------HOMEOBOX_2  PDB: C:343-395 UniProt: 335-395                  -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------HOMEOBOX_1              ---- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xsd C 247 APSSDDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLNKWLEETD-----------------------SIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP 397
                                   256       266       276       286       296       306       316  |      -         -      |346       356       366       376       386       396 
                                                                                                  319                     343                                                      

   Legend:   → Mismatch (orange background)
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    → 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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (PO3F1_MOUSE | P21952)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001105    RNA polymerase II transcription coactivator activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
    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.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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.
biological process
    GO:0014044    Schwann cell development    The process aimed at the progression of a Schwann cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0022011    myelination in peripheral nervous system    The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0010628    positive regulation of gene expression    Any process that increases 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: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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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: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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