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 :  CHROMO SHADOW DOMAIN FROM FISSION YEAST SWI6 PROTEIN.
 
Authors :  N. P. Cowieson, J. F. Partridge, R. C. Allshire, P. J. Mclaughlin
Date :  16 Mar 00  (Deposition) - 12 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chromatin-Binding, Chromodomain, Shadow, Heterochromatin, Swi6, Pombe (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. P. Cowieson, J. F. Partridge, R. C. Allshire, P. J. Mclaughlin
Dimerisation Of Chromo Shadow Domain And Distinctions From The Chromodomain As Revealed By Structural Analysis
Curr. Biol. V. 10 517 2000
PubMed-ID: 10801440  |  Reference-DOI: 10.1016/S0960-9822(00)00467-X

(-) Compounds

Molecule 1 - SWI6 PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentCHROMO SHADOW DOMAIN
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    Other DetailsRECOMBINANT PROTEIN OVEREXPRESSED IN ESCHERICHIA COLI.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:297 , HOH A:2054 , HOH A:2055 , HOH A:2057 , TRP B:293 , ASN B:295 , ALA B:297BINDING SITE FOR RESIDUE 1PG A 438

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E0B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E0B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E0B)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.SWI6_SCHPO81-143
267-328
 
  2-
A:267-322
B:267-324

(-) Exons   (0, 0)

(no "Exon" information available for 1E0B)

(-) 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:61
 aligned with SWI6_SCHPO | P40381 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:61
                                   271       281       291       301       311       321 
           SWI6_SCHPO   262 QVENYDSWEDLVSSIDTIERKDDGTLEIYLTWKNGAISHHPSTITNKKCPQKMLQFYESHL 322
               SCOP domains d1e0ba_ A: Heterochromatin protein 1, HP1                     SCOP domains
               CATH domains 1e0bA00 A:262-322  [code=2.40.50.40, no name defined]         CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee.eeee.....eeeeeee....eeeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----CHROMO_2  PDB: A:267-322 UniProt: 267-328                PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 1e0b A 262 QVENYDSWEDLVSSIDTIERKDDGTLEIYLTWKNGAISHHPSTITNKKCPQKMLQFYESHL 322
                                   271       281       291       301       311       321 

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with SWI6_SCHPO | P40381 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:59
                                   275       285       295       305       315         
           SWI6_SCHPO   266 YDSWEDLVSSIDTIERKDDGTLEIYLTWKNGAISHHPSTITNKKCPQKMLQFYESHLTF 324
               SCOP domains d1e0bb_ B: Heterochromatin protein 1, HP1                   SCOP domains
               CATH domains 1e0bB00 B:266-324  [code=2.40.50.40, no name defined]       CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.eeee.....eeeeeee....eeeeehhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CHROMO_2  PDB: B:267-324 UniProt: 267-328                  PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 1e0b B 266 YDSWEDLVSSIDTIERKDDGTLEIYLTWKNGAISHHPSTITNKKCPQKMLQFYESHLTF 324
                                   275       285       295       305       315         

   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
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E0B)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SWI6_SCHPO | P40381)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    GO:0031493    nucleosomal histone binding    Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
    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:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0030702    chromatin silencing at centromere    Repression of transcription of centromeric DNA by altering the structure of chromatin.
    GO:1990141    chromatin silencing at centromere outer repeat region    Repression of transcription of DNA at the outer repeat region of a regional centromere by altering the structure of chromatin.
    GO:0030466    chromatin silencing at silent mating-type cassette    Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
    GO:0006348    chromatin silencing at telomere    Repression of transcription of telomeric DNA by altering the structure of chromatin.
    GO:0072356    chromosome passenger complex localization to kinetochore    A cellular protein complex localization that acts on a chromosome passenger complex; as a result, the complex is transported to, or maintained in, a specific location at the kinetochore. A chromosome passenger complex is a protein complex that contains the BIR-domain-containing protein Survivin, Aurora B kinase, INCENP and Borealin, and coordinates various events based on its location to different structures during the course of mitosis.
    GO:0007535    donor selection    The process that determines which donor locus a cell uses, in preference to another, in mating type switching.
    GO:0007534    gene conversion at mating-type locus    The conversion of the mating-type locus from one allele to another resulting from the recombinational repair of a site-specific double-strand break at the mating-type locus with information from a silent donor sequence. There is no reciprocal exchange of information because the mating-type locus copies information from the donor sequence and the donor sequence remains unchanged.
    GO:0007533    mating type switching    The conversion of a single-cell organism from one mating type to another by the precise replacement of a DNA sequence at the expressed mating type locus with a copy of a sequence from a donor locus.
    GO:0007064    mitotic sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the entire length of the chromosome, from their formation in S phase through metaphase during a mitotic cell cycle. This cohesion cycle is critical for high fidelity chromosome transmission.
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    GO:0071459    protein localization to chromosome, centromeric region    Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome.
    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:0034507    chromosome, centromeric outer repeat region    The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000780    condensed nuclear chromosome, centromeric region    The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0031934    mating-type region heterochromatin    Heterochromatic regions of the chromosome found at silenced mating-type loci.
    GO:0044732    mitotic spindle pole body    The microtubule organizing center that forms as part of the mitotic cell cycle; functionally homologous to the animal cell centrosome.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    GO:0031618    nuclear pericentric heterochromatin    Nuclear heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    GO:1990707    nuclear subtelomeric heterochromatin    Heterochromatic regions of the chromosome found at the subtelomeric regions 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.
    GO:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.

 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
    1PG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1e0b)
 

(-) 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
  1e0b
    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
  SWI6_SCHPO | P40381
    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
  SWI6_SCHPO | P40381
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SWI6_SCHPO | P403812rso

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1E0B)