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

(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE SIR4P C-TERMINAL COILED COIL
 
Authors :  G. A. Murphy, E. J. Spedale, S. T. Powell, L. Pillus, S. C. Schultz, L. Chen
Date :  06 Jun 03  (Deposition) - 01 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,S
Keywords :  Parallel Coiled Coil Homodimer, Dna Binding Protein/Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. A. Murphy, E. J. Spedale, S. T. Powell, L. Pillus, S. C. Schultz, L. Chen
The Sir4 C-Terminal Coiled Coil Is Required For Telomeric And Mating Type Silencing In Saccharomyces Cerevisiae.
J. Mol. Biol. V. 334 769 2003
PubMed-ID: 14636601  |  Reference-DOI: 10.1016/J.JMB.2003.09.066
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN SIR4
    ChainsA, S
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKKT7E
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1217-1358
    GeneSIR4
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymSILENT INFORMATION REGULATOR 4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AS

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1PL5)

(-) Sites  (0, 0)

(no "Site" information available for 1PL5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PL5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PL5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PL5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PL5)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR227W1YDR227W.1IV:917568-9216444077SIR4_YEAST1-135813582A:1272-1346
S:1272-1347
75
76

(-) 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:75
 aligned with SIR4_YEAST | P11978 from UniProtKB/Swiss-Prot  Length:1358

    Alignment length:75
                                  1281      1291      1301      1311      1321      1331      1341     
          SIR4_YEAST   1272 SFVDIVLSKAASALDEKEKQLAVANEIIRSLSDEVMRNEIRITSLQGDLTFTKKCLENARSQISEKDAKINKLME 1346
               SCOP domains d1pl5a_ A: Dimerization motif of sir4                                       SCOP domains
               CATH domains 1pl5A00 A:1272-1346 Single helix bin                                        CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1272-1346 UniProt: 1-1358 [INCOMPLETE]                     Transcript 1
                1pl5 A 1272 SFVDIVLSKAASALDEKEKQLAVANEIIRSLSDEVMRNEIRITSLQGDLTFTKKCLENARSQISEKDAKINKLME 1346
                                  1281      1291      1301      1311      1321      1331      1341     

Chain S from PDB  Type:PROTEIN  Length:76
 aligned with SIR4_YEAST | P11978 from UniProtKB/Swiss-Prot  Length:1358

    Alignment length:76
                                  1281      1291      1301      1311      1321      1331      1341      
          SIR4_YEAST   1272 SFVDIVLSKAASALDEKEKQLAVANEIIRSLSDEVMRNEIRITSLQGDLTFTKKCLENARSQISEKDAKINKLMEK 1347
               SCOP domains d1pl5s_ S: Dimerization motif of sir4                                        SCOP domains
               CATH domains 1pl5S00 S:1272-1347 Single helix bin                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: S:1272-1347 UniProt: 1-1358 [INCOMPLETE]                      Transcript 1
                1pl5 S 1272 SFVDIVLSKAASALDEKEKQLAVANEIIRSLSDEVMRNEIRITSLQGDLTFTKKCLENARSQISEKDAKINKLMEK 1347
                                  1281      1291      1301      1311      1321      1331      1341      

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PL5)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,S   (SIR4_YEAST | P11978)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0031491    nucleosome binding    Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0001308    negative regulation of chromatin silencing involved in replicative cell aging    The process, which occurs as a dividing cell ages, leading to expression of genes that are typically not expressed due to silencing by regulatory proteins.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005677    chromatin silencing complex    Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.
    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 1pl5)
 
  Sites
(no "Sites" information available for 1pl5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pl5)
 

(-) 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
  1pl5
    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
  SIR4_YEAST | P11978
    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
  SIR4_YEAST | P11978
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SIR4_YEAST | P119781nyh 4iao

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PL5)