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 :  FBP28WW2 DOMAIN IN COMPLEX WITH THE PPLIPPPP PEPTIDE
 
Authors :  X. Ramirez-Espain, L. Ruiz, P. Martin-Malpartida, H. Oschkinat, M. J. Macias
Date :  01 Sep 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  P,W  (10x)
Keywords :  Fbp28Ww Domain, Pplipppp Peptide, Nmr, Alternative Splicing, Coiled Coil, Nucleus, Polymorphism, Repressor, Transcription, Transcription Regulation, Actin-Binding, Cell Junction, Cytoplasm, Membrane, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Ramirez-Espain, L. Ruiz, P. Martin-Malpartida, H. Oschkinat, M. J. Macias
Structural Characterization Of A New Binding Motif And A Novel Binding Mode In Group 2 Ww Domains
J. Mol. Biol. V. 373 1255 2007
PubMed-ID: 17915251  |  Reference-DOI: 10.1016/J.JMB.2007.08.052
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION ELONGATION REGULATOR 1
    ChainsW
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPETM30
    Expression System Vector TypeVECTOR
    FragmentWW 2 DOMAIN, SEQUENCE DATABASE RESIDUES 430-466
    GeneTCERG1, TAF2S
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTATA BOX-BINDING PROTEIN- ASSOCIATED FACTOR 2S, TRANSCRIPTION FACTOR CA150, P144, FORMIN- BINDING PROTEIN 28, FBP 28
 
Molecule 2 - FORMIN-1
    ChainsP
    EngineeredYES
    FragmentSEQUENCE DATABASE RESIDUES, 881-888
    Other DetailsTHE AUTHORS STATE THAT THE PEPTIDE WAS CHEMICALLY SYNTHESIZED AND THE SEQUENCE CORRESPONDS TO THE MOUSE FORMIN PROTEIN.
    SynonymLIMB DEFORMITY PROTEIN
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2JUP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_2PS50020 WW/rsp5/WWP domain profile.TCRG1_MOUSE131-164
431-464
534-563
  1-
W:2-35
-
2WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.TCRG1_MOUSE437-462  1W:8-33

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSMUST000000253751ENSMUSE00000246334chr18:42671141-4267123999TCRG1_MOUSE1-20200--
1.2ENSMUST000000253752ENSMUSE00000246318chr18:42679022-42679247226TCRG1_MOUSE20-95760--
1.3ENSMUST000000253753ENSMUSE00000142916chr18:42682568-42682720153TCRG1_MOUSE96-146510--
1.4ENSMUST000000253754ENSMUSE00000142910chr18:42683547-42684006460TCRG1_MOUSE147-3001540--
1.5ENSMUST000000253755ENSMUSE00000142917chr18:42690302-42690544243TCRG1_MOUSE300-381820--
1.6ENSMUST000000253756ENSMUSE00000142908chr18:42694739-4269480163TCRG1_MOUSE381-402220--
1.7ENSMUST000000253757ENSMUSE00000142915chr18:42695832-42696032201TCRG1_MOUSE402-469681W:1-3737
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 P from PDB  Type:PROTEIN  Length:9
 aligned with FMN1_MOUSE | Q05860 from UniProtKB/Swiss-Prot  Length:1466

    Alignment length:30
                                   868       878       888
           FMN1_MOUSE   859 GTSSSSQHKISPPAPPTPPPLPPPLIPPPP 888
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .---------------------........ Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 2jup P 101 G---------------------PPLIPPPP 109
                            |        -         -  |    109
                            |                   102       
                          101                             

Chain W from PDB  Type:PROTEIN  Length:37
 aligned with TCRG1_MOUSE | Q8CGF7 from UniProtKB/Swiss-Prot  Length:1100

    Alignment length:37
                                   439       449       459       
          TCRG1_MOUSE   430 GATAVSEWTEYKTADGKTYYYNNRTLESTWEKPQELK 466
               SCOP domains d2jupw1 W:1-37                        SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ----WW-2jupW01 W:5-33            ---- Pfam domains
         Sec.struct. author ...................eee....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                PROSITE (1) -WW_DOMAIN_2  PDB: W:2-35          -- PROSITE (1)
                PROSITE (2) -------WW_DOMAIN_1  PDB: W:8-33  ---- PROSITE (2)
               Transcript 1 Exon 1.7  PDB: W:1-37 [INCOMPLETE]    Transcript 1
                 2jup W   1 GATAVSEWTEYKTADGKTYYYNNRTLESTWEKPQELK  37
                                    10        20        30       

   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 2JUP)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (34, 35)

NMR Structure(hide GO term definitions)
Chain P   (FMN1_MOUSE | Q05860)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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).
biological process
    GO:0045010    actin nucleation    The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament. Nucleation is slow relative to the subsequent addition of more monomers to extend the filament.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0035136    forelimb morphogenesis    The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
    GO:0010467    gene expression    The process in which a gene's 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:0035137    hindlimb morphogenesis    The process in which the anatomical structures of the hindlimb are generated and organized.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0060173    limb development    The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:0051127    positive regulation of actin nucleation    Any process that activates or increases the frequency, rate or extent of actin nucleation, the initial step in the formation of an actin filament in which actin monomers combine to form a new filament.
    GO:0051894    positive regulation of focal adhesion assembly    Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    GO:0072092    ureteric bud invasion    The process in which the ureteric bud grows along its axis and contributes to the formation of the metanephros.
cellular component
    GO:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain W   (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 2jup)
 
  Sites
(no "Sites" information available for 2jup)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jup)
 

(-) 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
  2jup
    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
  FMN1_MOUSE | Q05860
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TCRG1_MOUSE | Q8CGF7
    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
  FMN1_MOUSE | Q05860
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TCRG1_MOUSE | Q8CGF7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FMN1_MOUSE | Q058602rly 2rm0
        TCRG1_MOUSE | Q8CGF71e0l 2rly 2rm0 2ysi

(-) Related Entries Specified in the PDB File

2rly
2rm0 RELATED ID: 15453 RELATED DB: BMRB