Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE 2ND CAP-GLY DOMAIN IN HUMAN RESTIN-LIKE PROTEIN 2 REVEALS A SWAPPED-DIMER
 
Authors :  K. Saito, S. Yoshikawa, A. Nishino, K. Murayama, T. Terada, M. Shirouzu, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  07 May 07  (Deposition) - 13 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cap-Gly Domain-Containing Linker Protein 4, Alternative Splicing, Ank Repeat, Protein Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Saito, S. Yoshikawa, A. Nishino, K. Murayama, T. Terada, M. Shirouzu, T. Kigawa, S. Yokoyama
Crystal Structure Of The 2Nd Cap-Gly Domain In Human Restin-Like Protein 2 Reveals A Swapped-Dimer
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAP-GLY DOMAIN-CONTAINING LINKER PROTEIN 4
    ChainsA
    EngineeredYES
    Expression System PlasmidPK040816-21
    Expression System Vector TypePLASMID
    FragmentCAP-GLY DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymRESTIN-LIKE PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Z0W)

(-) Sites  (0, 0)

(no "Site" information available for 2Z0W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z0W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048675R486LCLIP4_HUMANPolymorphism3100246AR12L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048675R486LCLIP4_HUMANPolymorphism3100246AR12L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CAP_GLY_2PS50245 CAP-Gly domain profile.CLIP4_HUMAN303-345
505-547
644-686
  1-
A:31-73
-
2CAP_GLY_1PS00845 CAP-Gly domain signature.CLIP4_HUMAN505-536
644-675
  1A:31-62
-
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CAP_GLY_2PS50245 CAP-Gly domain profile.CLIP4_HUMAN303-345
505-547
644-686
  2-
A:31-73
-
2CAP_GLY_1PS00845 CAP-Gly domain signature.CLIP4_HUMAN505-536
644-675
  2A:31-62
-

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000003200814aENSE00001836545chr2:29338292-29338531240CLIP4_HUMAN-00--
1.6aENST000003200816aENSE00002170039chr2:29344240-29344387148CLIP4_HUMAN1-45450--
1.9bENST000003200819bENSE00002182830chr2:29354124-29354263140CLIP4_HUMAN45-91470--
1.9dENST000003200819dENSE00001764666chr2:29355018-2935511194CLIP4_HUMAN92-123320--
1.10ENST0000032008110ENSE00001595204chr2:29356521-29356682162CLIP4_HUMAN123-177550--
1.11cENST0000032008111cENSE00001685160chr2:29358414-29358532119CLIP4_HUMAN177-216400--
1.12ENST0000032008112ENSE00001635650chr2:29366575-29366811237CLIP4_HUMAN217-295790--
1.13ENST0000032008113ENSE00001762009chr2:29368098-29368233136CLIP4_HUMAN296-341460--
1.14ENST0000032008114ENSE00001799287chr2:29375551-29375694144CLIP4_HUMAN341-389490--
1.15ENST0000032008115ENSE00001704942chr2:29379220-2937930990CLIP4_HUMAN389-419310--
1.16aENST0000032008116aENSE00001614395chr2:29380070-29380213144CLIP4_HUMAN419-467490--
1.17aENST0000032008117aENSE00001741223chr2:29383199-29383333135CLIP4_HUMAN467-512461A:11-3828
1.18bENST0000032008118bENSE00001800869chr2:29386697-29386820124CLIP4_HUMAN512-553421A:38-7942
1.19aENST0000032008119aENSE00001799791chr2:29390342-2939040665CLIP4_HUMAN553-575231A:79-824
1.20aENST0000032008120aENSE00001735118chr2:29397239-2939731173CLIP4_HUMAN575-599250--
1.22eENST0000032008122eENSE00001955568chr2:29404438-294066792242CLIP4_HUMAN599-7051070--

(-) Sequences/Alignments

Asymmetric Unit
   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:72
 aligned with CLIP4_HUMAN | Q8N3C7 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:72
                                   494       504       514       524       534       544       554  
          CLIP4_HUMAN   485 LRLGERVLVVGQRLGTIRFFGTTNFAPGYWYGIELEKPHGKNDGSVGGVQYFSCSPRYGIFAPPSRVQRVTD 556
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains --CAP_GLY-2z0wA01 A:13-78                                           ---- Pfam domains
         Sec.struct. author ..............eeeeeee........eeeeee.........ee..ee........eeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) -L---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------CAP_GLY_2  PDB: A:31-73 UniProt: 505-547   --------- PROSITE (1)
                PROSITE (2) --------------------CAP_GLY_1  PDB: A:31-62         -------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.17a  PDB: A:11-38    ----------------------------------------1.19 Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.18b  PDB: A:38-79 UniProt: 512-553 --- Transcript 1 (2)
                 2z0w A  11 LRLGERVLVVGQRLGTIRFFGTTNFAPGYWYGIELEKPHGKNDGSVGGVQYFSCSPRYGIFAPPSRVQRVTD  82
                                    20        30        40        50        60        70        80  

   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 2Z0W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z0W)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (CLIP4_HUMAN | Q8N3C7)
molecular function
    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).

 Visualization

(-) Interactive Views

Asymmetric Unit
  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 2z0w)
 
  Sites
(no "Sites" information available for 2z0w)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2z0w)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) 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
  2z0w
    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
  CLIP4_HUMAN | Q8N3C7
    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
  CLIP4_HUMAN | Q8N3C7
    Protein Disorder PredictionDisEMBL | 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 2Z0W)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Z0W)