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(-) Description

Title :  SOLUTION STRUCTURE OF THE CUT DOMAIN OF HUMAN HOMEOBOX PROTEIN CUX-2 (CUT-LIKE 2)
 
Authors :  Y. O. Kamatari, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 05  (Deposition) - 26 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cut Domain, Human Homeobox Protein Cux-2, Cut-Like 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 :  Y. O. Kamatari, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Cut Domain Of Human Homeobox Protein Cux-2 (Cut-Like 2)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMEOBOX PROTEIN CUX-2
    ChainsA
    EngineeredYES
    Expression System PlasmidP040531-01
    Expression System Vector TypePLASMID
    FragmentCUT DOMAIN
    GeneCUTL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymCUT-LIKE 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 1X2L)

(-) Sites  (0, 0)

(no "Site" information available for 1X2L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X2L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X2L)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUTPS51042 CUT domain profile.CUX2_HUMAN544-631
887-974
1038-1125
  1A:8-95
-
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002617261ENSE00001128994chr12:111471829-111472044216CUX2_HUMAN1-21210--
1.5bENST000002617265bENSE00001775253chr12:111652004-111652114111CUX2_HUMAN22-58370--
1.6ENST000002617266ENSE00001766284chr12:111655694-11165574148CUX2_HUMAN59-74160--
1.7ENST000002617267ENSE00000998067chr12:111701565-11170164379CUX2_HUMAN75-101270--
1.8ENST000002617268ENSE00000998068chr12:111729222-111729356135CUX2_HUMAN101-146460--
1.9ENST000002617269ENSE00001213639chr12:111731250-111731373124CUX2_HUMAN146-187420--
1.10bENST0000026172610bENSE00001299235chr12:111733137-11173321377CUX2_HUMAN187-213270--
1.11ENST0000026172611ENSE00000938106chr12:111734277-11173434367CUX2_HUMAN213-235230--
1.12ENST0000026172612ENSE00000755136chr12:111736345-11173639349CUX2_HUMAN235-251170--
1.13ENST0000026172613ENSE00000755138chr12:111742014-111742118105CUX2_HUMAN252-286350--
1.14ENST0000026172614ENSE00000755140chr12:111744725-111744916192CUX2_HUMAN287-350640--
1.15ENST0000026172615ENSE00000755142chr12:111745003-11174506159CUX2_HUMAN351-370200--
1.16ENST0000026172616ENSE00000755143chr12:111746089-11174613749CUX2_HUMAN370-386170--
1.17ENST0000026172617ENSE00000755144chr12:111746231-111746330100CUX2_HUMAN387-420340--
1.18ENST0000026172618ENSE00000834831chr12:111747845-111748486642CUX2_HUMAN420-6342151A:1-97 (gaps)103
1.19ENST0000026172619ENSE00001309503chr12:111749904-111750005102CUX2_HUMAN634-668351A:97-101 (gaps)13
1.20ENST0000026172620ENSE00001293611chr12:111757816-111758579764CUX2_HUMAN668-9222550--
1.21ENST0000026172621ENSE00001301644chr12:111760225-111760384160CUX2_HUMAN923-976540--
1.22ENST0000026172622ENSE00001329663chr12:111772245-111772514270CUX2_HUMAN976-1066910--
1.23ENST0000026172623ENSE00001310756chr12:111776090-111776278189CUX2_HUMAN1066-1129640--
1.24ENST0000026172624ENSE00001292378chr12:111779584-111779857274CUX2_HUMAN1129-1220920--
1.25bENST0000026172625bENSE00001314718chr12:111785328-1117883563029CUX2_HUMAN1220-14862670--

(-) 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 CUX2_HUMAN | O14529 from UniProtKB/Swiss-Prot  Length:1486

    Alignment length:115
                                   541       551       561       571       581       591       601       611       621       631       641     
           CUX2_HUMAN   532 GPEPADGGGGGAAGPGAEEEQLDTAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKLTVKGKEPFIKMKQFLSDEQNVLALRTIQVRQRGSITPRIRTPETG 646
               SCOP domains -------------d1x2la1 A:9-95 Homeobox protein Cux-2, CUTL2                                           --------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------CUT-1x2lA01 A:11-33    ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---......--..........hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.-.--------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------CUT  PDB: A:8-95 UniProt: 544-631                                                       --------------- PROSITE
           Transcript 1 (1) Exon 1.18  PDB: A:1-97 (gaps) UniProt: 420-634 [INCOMPLETE]                                            ------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------Exon 1.19     Transcript 1 (2)
                 1x2l A   1 G---SSGSSG--AGPGAEEEQLDTAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKLTVKGKEPFIKMKQFLSDEQNVLALRTIQVRS-G--------PSSG 101
                            |   |    7  |     15        25        35        45        55        65        75        85        95| |      - |   
                            |   2    7  8                                                                                      96 |       98   
                            1                                                                                                    97            

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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  (0, 0)

(no "CATH Domain" information available for 1X2L)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (CUX2_HUMAN | O14529)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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:0001078    transcriptional repressor 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    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:0050890    cognition    The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
    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: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:0050775    positive regulation of dendrite morphogenesis    Any process that activates or increases the frequency, rate or extent of dendrite morphogenesis.
    GO:0061003    positive regulation of dendritic spine morphogenesis    Any process that increases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:2000463    positive regulation of excitatory postsynaptic potential    Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    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:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007614    short-term memory    The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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: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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        CUX2_HUMAN | O145291wh6 1wh8

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