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

(-) Description

Title :  CRYSTAL STRUCTURE OF S. POMBE STN1-TEN1 COMPLEX
 
Authors :  J. Sun, E. Y. Yu, Y. T. Yang, L. A. Confer, S. H. Sun, K. Wan, N. F. Lue, M. Lei
Date :  27 Oct 09  (Deposition) - 22 Dec 09  (Release) - 29 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ob Fold, Chromosomal Protein, Dna-Binding, Nucleus, Telomere (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Sun, E. Y. Yu, Y. Yang, L. A. Confer, S. H. Sun, K. Wan, N. F. Lue, M. Lei
Stn1-Ten1 Is An Rpa2-Rpa3-Like Complex At Telomeres.
Genes Dev. V. 23 2900 2009
PubMed-ID: 20008938  |  Reference-DOI: 10.1101/GAD.1851909
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN STN1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSTN1, SPBC409.12C
    Organism CommonYEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
 
Molecule 2 - PROTEIN TEN1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 2-102
    GeneTEN1, SPCC1393.14
    Organism CommonYEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3KF6)

(-) Sites  (0, 0)

(no "Site" information available for 3KF6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KF6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KF6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KF6)

(-) Exons   (0, 0)

(no "Exon" information available for 3KF6)

(-) 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:136
 aligned with STN1_SCHPO | Q0E7J7 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:139
                                    25        35        45        55        65        75        85        95       105       115       125       135       145         
           STN1_SCHPO    16 SRWNPMFISDVHKISFHPHLQRYIGFWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVLRVVFIIQDDFSMSKRAISMSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQKRMRYKKNLTKISKNHH 154
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Stn1-3kf6A01 A:16-1   54                                                                                                                    Pfam domains
         Sec.struct. author ......hhhhhh.......---..eee..eee.eeeeeeeeeeeeee..eeeeeee.....eeeeeee...hhhhhhhhh......eeeeeeeee......eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kf6 A  16 SRWNPMFISDVHKISFHPH---YIGFWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVLRVVFIIQDDFSMSKRAISMSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQKRMRYKKNLTKISKNHH 154
                                    25        |-  |     45        55        65        75        85        95       105       115       125       135       145         
                                             34  38                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with TEN1_SCHPO | P0C5Y7 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:105
                               1                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97     
           TEN1_SCHPO     - ---MDSAKLIFINQINDCKDGQKLRFLGCVQSYKNGILRLIDGSSSVTCDVTVVLPDVSIQKHEWLNIVGRKRQDGIVDVLLIRSAVGINLPRYRQMVSERQKCD 102
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Ten1-3kf6B01 B:502-596                                                                         ------ Pfam domains
         Sec.struct. author .......ee.hhhhhhhh....eeeeeeeeeeee..eeeeee..eeeeee..............eeeeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3kf6 B 498 PLGSDSAKLIFINQINDCKDGQKLRFLGCVQSYKNGILRLIDGSSSVTCDVTVVLPDVSIQKHEWLNIVGRKRQDGIVDVLLIRSAVGINLPRYRQMVSERQKCD 602
                                   507       517       527       537       547       557       567       577       587       597     

   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 3KF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KF6)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (10, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (STN1_SCHPO | Q0E7J7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
cellular component
    GO:1990879    CST complex    A complex formed by the association of Cdc13 (CTC1 in mammals) with Stn1 in yeast (OBFC1 in mammals) and Ten1 protein (also TEN1 in mammals) with single-stranded telomeric DNA. The CST complex plays a role in telomere protection.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005724    nuclear telomeric heterochromatin    Heterochromatic regions of the chromosome found at the telomeres of a chromosome in the nucleus.
    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.

Chain B   (TEN1_SCHPO | P0C5Y7)
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).
    GO:0043047    single-stranded telomeric DNA binding    Interacting selectively and non-covalently with single-stranded telomere-associated DNA.
biological process
    GO:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
cellular component
    GO:1990879    CST complex    A complex formed by the association of Cdc13 (CTC1 in mammals) with Stn1 in yeast (OBFC1 in mammals) and Ten1 protein (also TEN1 in mammals) with single-stranded telomeric DNA. The CST complex plays a role in telomere protection.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005724    nuclear telomeric heterochromatin    Heterochromatic regions of the chromosome found at the telomeres of a chromosome in the nucleus.
    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

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
(no "Ligands, Modified Residues, Ions" information available for 3kf6)
 
  Sites
(no "Sites" information available for 3kf6)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kf6)
 

(-) 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
  3kf6
    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
  STN1_SCHPO | Q0E7J7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TEN1_SCHPO | P0C5Y7
    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
  STN1_SCHPO | Q0E7J7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TEN1_SCHPO | P0C5Y7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TEN1_SCHPO | P0C5Y73k0x

(-) Related Entries Specified in the PDB File

3key CRYSTAL STRUCTURE OF S. CEREVISIAE STN1 C-TERMINAL
3kf8 CRYSTAL STRUCTURE OF C. TROPICALIS STN1-TEN1 COMPLEX