Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE THIRD CUT DOMAIN OF HUMAN HOMEOBOX PROTEIN CUX-2
 
Authors :  N. Nameki, N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cut Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Nameki, N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of The Third Cut Domain Of Human Homeobox Protein Cux-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 PlasmidP040114-59
    Expression System Vector TypePLASMID
    FragmentCUT DOMAIN
    GeneKAZUSA CDNA HG03205
    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 1WH8)

(-) Sites  (0, 0)

(no "Site" information available for 1WH8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WH8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WH8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WH8)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUTPS51042 CUT domain profile.CUX2_HUMAN544-631
887-974
1038-1125
  1-
-
A:18-105

(-) Exons   (3, 3)

NMR Structure (3, 3)
 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_HUMAN420-6342150--
1.19ENST0000026172619ENSE00001309503chr12:111749904-111750005102CUX2_HUMAN634-668350--
1.20ENST0000026172620ENSE00001293611chr12:111757816-111758579764CUX2_HUMAN668-9222550--
1.21ENST0000026172621ENSE00001301644chr12:111760225-111760384160CUX2_HUMAN923-976540--
1.22ENST0000026172622ENSE00001329663chr12:111772245-111772514270CUX2_HUMAN976-1066911A:1-46 (gaps)50
1.23ENST0000026172623ENSE00001310756chr12:111776090-111776278189CUX2_HUMAN1066-1129641A:46-10863
1.24ENST0000026172624ENSE00001292378chr12:111779584-111779857274CUX2_HUMAN1129-1220921A:109-1113
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:111
 aligned with CUX2_HUMAN | O14529 from UniProtKB/Swiss-Prot  Length:1486

    Alignment length:125
                                  1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136     
          CUX2_HUMAN   1017 GRSSSSLSGKMYSGSQAPGGIQEIVAMSPELDTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQLWLNDPHNVEKLRDMKKLEKKAYLKRRYGLISTG 1141
               SCOP domains d1wh8  a_   A: Homeobox protein Cux-2, CUTL2                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------CUT-1wh8A01 A:19-43      ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....--..--........hhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhh....----------... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------CUT  PDB: A:18-105 UniProt: 1038-1125                                                   ---------------- PROSITE
           Transcript 1 (1) Exon 1.22  PDB: A:1-46 (gaps) UniProt: 976-1066   --------------------------------------------------------------Exon 1.24     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.23  PDB: A:46-108 UniProt: 1066-1129 [INCOMPLETE]        ------------ Transcript 1 (2)
                1wh8 A    1 GSSGS--SG--YSGSQAPGGIQEIVAMSPELDTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQLWLNDPHNVEKLRDMKKLSGP----------SSG  111
                                |  ||- |      16        26        36        46        56        66        76        86        96       106 |       -  |  
                                5  6|  8                                                                                                 108        109  
                                    7                                                                                                                    

   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 1WH8)

(-) 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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1wh8)
 
  Sites
(no "Sites" information available for 1wh8)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wh8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1wh8
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CUX2_HUMAN | O14529
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CUX2_HUMAN | O14529
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CUX2_HUMAN | O145291wh6 1x2l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WH8)