Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
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 NOVEL IDENTIFIED UBIQUITIN-LIKE DOMAIN IN THE HUMAN COBL-LIKE 1 PROTEIN
 
Authors :  C. Zhao, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Dec 05  (Deposition) - 14 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cobl-Like 1, Kiaa0977 Protein, Ubiquitin-Like Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhao, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Novel Identified Ubiquitin-Like Domain In The Human Cobl-Like 1 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA0977 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: P050719-08
    Expression System Vector Type: PLASMID
    Fragment: UBIQUITIN-LIKE DOMAIN
    Gene: KIAA0977
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: COBL-LIKE 1

 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 2DAJ)

(-) Sites  (0, 0)

(no "Site" information available for 2DAJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DAJ)

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3dENST000003927173dENSE00002197389chr2:165698535-16569846769COBL1_HUMAN1-22220--
1.4dENST000003927174dENSE00001739458chr2:165697756-16569766691COBL1_HUMAN22-52310--
1.11cENST0000039271711cENSE00001130123chr2:165600385-165600197189COBL1_HUMAN52-115641A:1-22
1.13cENST0000039271713cENSE00000779623chr2:165586625-165586424202COBL1_HUMAN115-182681A:2-8 (gaps)68
1.14dENST0000039271714dENSE00000779622chr2:165584707-165584479229COBL1_HUMAN183-259771A:9-8577
1.16cENST0000039271716cENSE00000779621chr2:165579032-16557893598COBL1_HUMAN259-291331A:85-851
1.17bENST0000039271717bENSE00000779620chr2:165578821-165578585237COBL1_HUMAN292-370791A:86-916
1.18bENST0000039271718bENSE00001687870chr2:165561615-165561462154COBL1_HUMAN371-422520--
1.19ENST0000039271719ENSE00000779618chr2:165561028-16556095475COBL1_HUMAN422-447260--
1.21ENST0000039271721ENSE00001628860chr2:165559730-165559614117COBL1_HUMAN447-486400--
1.22dENST0000039271722dENSE00001240267chr2:165557266-165557032235COBL1_HUMAN486-564790--
1.23ENST0000039271723ENSE00000779615chr2:165556009-16555591595COBL1_HUMAN564-596330--
1.24cENST0000039271724cENSE00001402586chr2:165552343-1655507791565COBL1_HUMAN596-11175220--
1.26aENST0000039271726aENSE00000525221chr2:165548907-165548731177COBL1_HUMAN1118-1176590--
1.27cENST0000039271727cENSE00001733988chr2:165542542-1655413271216COBL1_HUMAN1177-1204280--

(-) 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:91
 aligned with COBL1_HUMAN | Q53SF7 from UniProtKB/Swiss-Prot  Length:1204

    Alignment length:186
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
          COBL1_HUMAN   114 GSKPMMDLLIFLCAQYHLNPSSYTIDLLSAEQNHIKFKPNTPIGMLEVEKVILKPKMLDKKKPTPIIPEKTVRVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQSQEPLDLTKSLNDLGLRELYAMDVNRESCQISQNLDIMKEKENKGFFSFFQRSKKKRDQTASAPATP 299
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..----------------....---------------------------------------------....eeeeeee...eeeeeee....hhhhhhhhhhhhh......eeee.............hhhhhh..eeeeee....----------------------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.-------------------------------------------------------------------Exon 1.14d  PDB: A:9-85 UniProt: 183-259                                     --------------------------------1.17b    Transcript 1 (1)
           Transcript 1 (2) -Exon 1.13c  PDB: A:2-8 (gaps) UniProt: 115-182                      ----------------------------------------------------------------------------Exon 1.16c  PDB: A:85-85         -------- Transcript 1 (2)
                 2daj A   1 GS----------------SGSS---------------------------------------------GEKTVRVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQSQEPLDLTKSLNDLGLRELYAMDVNRE----------------------------------SGPSSG  91
                             |       -        |4 |       -         -         -         -       | 9        19        29        39        49        59        69        79     |   -         -         -         -|     
                             2                3  6                                             7                                                                            85                                 86
   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  (0, 0)

(no "SCOP Domain" information available for 2DAJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DAJ)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (COBL1_HUMAN | Q53SF7)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0003785    actin monomer binding    Interacting selectively and non-covalently with monomeric actin, also known as G-actin.
biological process
    GO:0051639    actin filament network formation    The assembly of a network of actin filaments; actin filaments on different axes and with differing orientations are crosslinked together to form a mesh of filaments.
    GO:0030041    actin filament polymerization    Assembly of actin filaments by the addition of actin monomers to a filament.
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.

 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 2daj)
 
  Sites
(no "Sites" information available for 2daj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2daj)
 

(-) 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
  2daj
    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
  COBL1_HUMAN | Q53SF7
    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
  COBL1_HUMAN | Q53SF7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2DAJ)

(-) Related Entries Specified in the PDB File

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