Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE N-TERMINAL DOMAIN OF C. ELEGANS SAS-6
 
Authors :  I. Vakonakis, M. O. Steinmetz
Date :  13 Dec 10  (Deposition) - 09 Feb 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Sandwich, Dimer, Alpha-Beta Protein, Structural Protein, Cytoplasmic, Centriolar (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Kitagawa, I. Vakonakis, N. Olieric, M. Hilbert, D. Keller, V. Olieric, M. Bortfeld, M. C. Erat, I. Fluckiger, P. Gonczy, M. O. Steinmetz
Structural Basis Of The 9-Fold Symmetry Of Centrioles.
Cell(Cambridge, Mass. ) V. 144 364 2011
PubMed-ID: 21277013  |  Reference-DOI: 10.1016/J.CELL.2011.01.008

(-) Compounds

Molecule 1 - SPINDLE ASSEMBLY ABNORMAL PROTEIN 6
    ChainsB, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN, UNP RESIDUES 1-168
    GeneSAS-6, Y45F10D.9
    MutationYES
    Organism CommonNEMATODE
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:142 , ALA A:166 , ARG A:168 , LEU B:22 , ASN B:23 , PRO B:25 , GLU B:140 , HOH B:175BINDING SITE FOR RESIDUE PG4 B 169
2AC2SOFTWARELYS B:31 , ARG B:42 , THR B:45 , SER B:46 , GLY B:47 , HOH B:218BINDING SITE FOR RESIDUE MES B 170
3AC3SOFTWARELEU B:98 , CYS B:100 , THR B:131BINDING SITE FOR RESIDUE PG4 B 171
4AC4SOFTWAREPRO A:19 , ILE A:136 , LEU A:137 , SER A:145BINDING SITE FOR RESIDUE PG4 A 169
5AC5SOFTWARELEU A:7 , ASP A:9 , GLN A:10 , CYS A:100 , LYS B:101BINDING SITE FOR RESIDUE PG4 A 170

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PYI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PYI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PYI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PYI)

(-) Exons   (0, 0)

(no "Exon" information available for 3PYI)

(-) Sequences/Alignments

Asymmetric/Biological 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:142
 aligned with SAS6_CAEEL | O62479 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
           SAS6_CAEEL     2 TSKIALFDQTLIASLLQPLSLNQPDFKAYKTKVKLKISEQRNETSGEKELKFEISRSDDFEFLFSETLNNEKYQILARDHDLTVDFDAFPKVIIQHLLCKNIVKNLEEDGEVDARKKAGYHSIADPGKPTEINIILDAEKNFCSFELFSKTPISKGKIFSIKLHAVR 168
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee......eeeeeeee.......eeeeeehhhhhhhhhhhhh......hhhhhhhhhhhhhhh.-------------------------.eeeeeee.....eeeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pyi A   2 TSKIALFDQTLIASLLQPLSLNQPDFKAYKTKVKLKISEQRNETSGEKELKFEISRSDDFEFLFSETLNNEKYQILARDHDLTVDFDAFPKVIIQHLLCKNIV-------------------------PTEINIILDAEKNFCSFELFSKTPISKGKIFSIKLHAVR 168
                                    11        21        31        41        51        61        71        81        91       101  |      -         -       131       141       151       161       
                                                                                                                                104                       130                                      

Chain B from PDB  Type:PROTEIN  Length:143
 aligned with SAS6_CAEEL | O62479 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:165
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
           SAS6_CAEEL     3 SKIALFDQTLIASLLQPLSLNQPDFKAYKTKVKLKISEQRNETSGEKELKFEISRSDDFEFLFSETLNNEKYQILARDHDLTVDFDAFPKVIIQHLLCKNIVKNLEEDGEVDARKKAGYHSIADPGKPTEINIILDAEKNFCSFELFSKTPISKGKIFSIKLHAV 167
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee......eeeeeeee.......eeeeeehhhhhhhhhhhhh......hhhhhhhhhh.......----------------------...eeeeeee.....eeeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pyi B   3 SKIALFDQTLIASLLQPLSLNQPDFKAYKTKVKLKISEQRNETSGEKELKFEISRSDDFEFLFSETLNNEKYQILARDHDLTVDFDAFPKVIIQHLLCKNIVK----------------------GKPTEINIILDAEKNFCSFELFSKTPISKGKIFSIKLHAV 167
                                    12        22        32        42        52        62        72        82        92       102  |      -         -     | 132       142       152       162     
                                                                                                                                105                    128                                       

   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 3PYI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PYI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PYI)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SAS6_CAEEL | O62479)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007099    centriole replication    The cell cycle process in which a daughter centriole is formed perpendicular to an existing centriole. An immature centriole contains a ninefold radially symmetric array of single microtubules; mature centrioles consist of a radial array of nine microtubule triplets, doublets, or singlets depending upon the species and cell type. Duplicated centrioles also become the ciliary basal body in cells that form cilia during G0.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    GO:0005814    centriole    A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pyi)
 

(-) 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
  3pyi
    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
  SAS6_CAEEL | O62479
    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
  SAS6_CAEEL | O62479
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SAS6_CAEEL | O624794g79 4geu 4gex 4gfa 4gfc 4gkw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PYI)