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 2ND CAP-GLY DOMAIN IN HUMAN CLIP-115/CYLN2
 
Authors :  K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  19 May 05  (Deposition) - 19 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Microtubule Binding, Cytoskeleton Associated Protein, Cyln2, Kiaa0291, 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 :  K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The 2Nd Cap-Gly Domain In Human Clip-115/Cyln2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLIP-115
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040301-94
    Expression System Vector Type: PLASMID
    Fragment: CAP-GLY DOMAIN
    Gene: KAZUSA CDNA FH25236
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: KIAA0291

 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 2CP3)

(-) Sites  (0, 0)

(no "Site" information available for 2CP3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CP3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CP3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CP3)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CAP_GLY_1PS00845 CAP-Gly domain signature.CLIP2_HUMAN99-130
239-270		  1-
A:28-59
2CAP_GLY_2PS50245 CAP-Gly domain profile.CLIP2_HUMAN99-141
239-281		  1-
A:28-70

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003950602bENSE00001520448chr7:73731877-73731997121CLIP2_HUMAN1-41410--
1.3ENST000003950603ENSE00001148434chr7:73752778-73753334557CLIP2_HUMAN41-2261861A:1-15 (gaps)28
1.4ENST000003950604ENSE00001148424chr7:73768210-73768334125CLIP2_HUMAN227-268421A:16-5742
1.5ENST000003950605ENSE00001148414chr7:73770740-73770953214CLIP2_HUMAN268-339721A:57-84 (gaps)51
1.6ENST000003950606ENSE00001148509chr7:73771610-73771807198CLIP2_HUMAN340-405660--
1.7ENST000003950607ENSE00001148497chr7:73774505-73774608104CLIP2_HUMAN406-440350--
1.8ENST000003950608ENSE00001148405chr7:73778585-7377864561CLIP2_HUMAN440-460210--
1.9ENST000003950609ENSE00001039278chr7:73787262-73787366105CLIP2_HUMAN461-495350--
1.10aENST0000039506010aENSE00000691493chr7:73790217-73791152936CLIP2_HUMAN496-8073120--
1.11bENST0000039506011bENSE00000691492chr7:73795136-7379519358CLIP2_HUMAN808-827200--
1.13cENST0000039506013cENSE00001148400chr7:73800851-7380093484CLIP2_HUMAN827-855290--
1.14cENST0000039506014cENSE00001148391chr7:73803433-73803589157CLIP2_HUMAN855-907530--
1.15cENST0000039506015cENSE00001148381chr7:73811404-73811563160CLIP2_HUMAN907-960540--
1.16aENST0000039506016aENSE00000691488chr7:73814700-73814885186CLIP2_HUMAN961-1022620--
1.17ENST0000039506017ENSE00001400047chr7:73815835-7381589763CLIP2_HUMAN1023-1043210--
1.18aENST0000039506018aENSE00001640935chr7:73818167-7381817812CLIP2_HUMAN1044-104630--

(-) 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:84
 aligned with CLIP2_HUMAN | Q9UDT6 from UniProtKB/Swiss-Prot  Length:1046

    Alignment length:120
                                   208       218       228       238       248       258       268       278       288       298       308       318
          CLIP2_HUMAN   199 GNESGSNLSDSGSVKRGEKDLRLGDRVLVGGTKTGVVRYVGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCPPKFGLFAPIHKVIRIGFPSTSPAKAKKTKRMAMGVSALTHSPSSS 318
               SCOP domains --------------------d2cp3a1 A:8-78 CLIP-115                                                ----------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-...----..--------.....eeee...eeeeeeeeee......eeeeeee.........ee..ee........eeeee...eee..-----------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------CAP_GLY_2  PDB: A:28-70 UniProt: 239-281   ------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------CAP_GLY_1  PDB: A:28-59         ------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:1-15 (gaps)Exon 1.4  PDB: A:16-57 UniProt: 227-268   -------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.5  PDB: A:57-84 (gaps) UniProt: 268-339      Transcript 1 (2)
                 2cp3 A   1 GS-SGS----SG--------LRLGDRVLVGGTKTGVVRYVGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCPPKFGLFAPIHKVIRIG-----------------------SGPSSG  84
                             | | |   -||       -|       17        27        37        47        57        67        77|        -         -    |   84
                             2 3 5    6|        8                                                                    78                      79     
                                       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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CP3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CP3)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (CLIP2_HUMAN | Q9UDT6)
molecular function
    GO:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    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:1901588    dendritic microtubule    Any microtubule in a dendrite, a neuron projection.
    GO:0042599    lamellar body    A membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0035371    microtubule plus-end    The growing (plus) end of a microtubule. In vitro, microtubules polymerize more quickly at the plus end than at the minus end. In vivo, microtubule growth occurs only at the plus end, and the plus end switches between periods of growth and shortening, a behavior known as dynamic instability.

 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 2cp3)
 
  Sites
(no "Sites" information available for 2cp3)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cp3)
 

(-) 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
  2cp3
    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
  CLIP2_HUMAN | Q9UDT6
    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
  CLIP2_HUMAN | Q9UDT6
    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
        CLIP2_HUMAN | Q9UDT6: 2cp2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CP3)