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 FIRST WW DOMAIN FROM THE MOUSE TRANSCRIPTION ELONGATION REGULATOR 1, TRANSCRIPTION FACTOR CA150
 
Authors :  S. Ohnishi, H. Li, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Transcription Elongation Regulator 1, Ca150, Fbp28, Ww Domain, Nmr, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ohnishi, H. Li, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama
Solution Structure Of The First Ww Domain From The Mouse Transcription Elongation Regulator 1, Transcription Factor Ca150
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION ELONGATION REGULATOR 1
    Chains: A
    Engineered: YES
    Expression System Plasmid: P070213-08
    Expression System Vector Type: PLASMID
    Fragment: WW DOMAIN
    Gene: TCERG1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR 2S, TRANSCRIPTION FACTOR CA150, P144, FORMIN-BINDING PROTEIN 28, FBP 28

 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 2YSI)

(-) Sites  (0, 0)

(no "Site" information available for 2YSI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_2PS50020 WW/rsp5/WWP domain profile.TCRG1_MOUSE131-164
431-464
534-563		  1A:8-39
-
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSMUST000000253751ENSMUSE00000246334chr18:42671141-4267123999TCRG1_MOUSE1-20200--
1.2ENSMUST000000253752ENSMUSE00000246318chr18:42679022-42679247226TCRG1_MOUSE20-95760--
1.3ENSMUST000000253753ENSMUSE00000142916chr18:42682568-42682720153TCRG1_MOUSE96-146511A:1-21 (gaps)25
1.4ENSMUST000000253754ENSMUSE00000142910chr18:42683547-42684006460TCRG1_MOUSE147-3001541A:22-4019
1.5ENSMUST000000253755ENSMUSE00000142917chr18:42690302-42690544243TCRG1_MOUSE300-381820--
1.6ENSMUST000000253756ENSMUSE00000142908chr18:42694739-4269480163TCRG1_MOUSE381-402220--
1.7ENSMUST000000253757ENSMUSE00000142915chr18:42695832-42696032201TCRG1_MOUSE402-469680--
1.8ENSMUST000000253758ENSMUSE00000142909chr18:42696516-42696628113TCRG1_MOUSE469-506380--
1.9ENSMUST000000253759ENSMUSE00000142918chr18:42697622-4269771089TCRG1_MOUSE507-536300--
1.10ENSMUST0000002537510ENSMUSE00000142907chr18:42708051-42708211161TCRG1_MOUSE536-590550--
1.11ENSMUST0000002537511ENSMUSE00000142912chr18:42709492-4270954857TCRG1_MOUSE590-609200--
1.12ENSMUST0000002537512ENSMUSE00000142914chr18:42709696-4270976267TCRG1_MOUSE609-631230--
1.13ENSMUST0000002537513ENSMUSE00000246134chr18:42712146-42712281136TCRG1_MOUSE631-676460--
1.14ENSMUST0000002537514ENSMUSE00000246118chr18:42713062-4271315190TCRG1_MOUSE677-706300--
1.15ENSMUST0000002537515ENSMUSE00000246090chr18:42720588-42720706119TCRG1_MOUSE707-746400--
1.16ENSMUST0000002537516ENSMUSE00000246066chr18:42723737-42723887151TCRG1_MOUSE746-796510--
1.17ENSMUST0000002537517ENSMUSE00000246042chr18:42727525-42727689165TCRG1_MOUSE797-851550--
1.18ENSMUST0000002537518ENSMUSE00000246017chr18:42728082-42728264183TCRG1_MOUSE852-912610--
1.19ENSMUST0000002537519ENSMUSE00000245983chr18:42730669-42730848180TCRG1_MOUSE913-972600--
1.20ENSMUST0000002537520ENSMUSE00000245943chr18:42731478-4273156184TCRG1_MOUSE973-1000280--
1.21ENSMUST0000002537521ENSMUSE00000458574chr18:42732914-42733014101TCRG1_MOUSE1001-1034340--
1.22ENSMUST0000002537522ENSMUSE00000480281chr18:42734172-427354391268TCRG1_MOUSE1034-1100670--

(-) 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:40
 aligned with TCRG1_MOUSE | Q8CGF7 from UniProtKB/Swiss-Prot  Length:1100

    Alignment length:44
                                   131       141       151       161    
          TCRG1_MOUSE   122 GTAPGAPALPPTEEIWVENKTPDGKVYYYNARTRESAWTKPDGV 165
               SCOP domains d2y sia_    A: automated matches             SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -----------WW-2ysiA01 A:8-37             --- Pfam domains
         Sec.struct. author ...-....---....eeeee.....eeeee.....ee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE ---------WW_DOMAIN_2  PDB: A:8-39          - PROSITE
               Transcript 1 Exon 1.3 UniProt: 96-146 Exon 1.4            Transcript 1
                 2ysi A   1 GSS-GSSG---TEEIWVENKTPDGKVYYYNARTRESAWTKPDGV  40
                              | |  | - |      16        26        36    
                              3 4  7   8
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: WW] (77)

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (TCRG1_MOUSE | Q8CGF7)
molecular function
    GO:0001103    RNA polymerase II repressing transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
    GO:0001106    RNA polymerase II transcription corepressor activity    Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0070064    proline-rich region binding    Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
    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: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: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:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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 2ysi)
 
  Sites
(no "Sites" information available for 2ysi)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ysi)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ysi
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TCRG1_MOUSE | Q8CGF7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TCRG1_MOUSE | Q8CGF7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TCRG1_MOUSE | Q8CGF7: 1e0l 2jup 2rly 2rm0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YSI)