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 ANALYSIS OF TRF2-DBD-DNA COMPLEX
 
Authors :  S. K. Nair, S. K. Sliverman, J. H. Chen, Y. Xiao
Date :  21 Jun 11  (Deposition) - 31 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Human Telomeric Repeat Binding Protein 2, Telomere, Telomeric Repeat, Homeodomain Proteins Amino Acid Sequence, Nucleic Acid, Dna-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. K. Nair, S. K. Sliverman, J. H. Chen, Y. Xiao
Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*GP*A)-3')
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 3 - TELOMERIC REPEAT-BINDING FACTOR 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B/THROMBIN
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTELOMERIC REPEAT BINDING FACTOR 2, TERF2, TRBF2, TRF2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTTAGGG REPEAT-BINDING FACTOR 2, TELOMERIC DNA-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3SJM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002549421ENSE00001141462chr16:69419859-69419496364TERF2_HUMAN1-85850--
1.2ENST000002549422ENSE00000904627chr16:69419389-6941929496TERF2_HUMAN85-117330--
1.3ENST000002549423ENSE00000904625chr16:69418613-69418483131TERF2_HUMAN117-160440--
1.4ENST000002549424ENSE00000904623chr16:69406258-6940617287TERF2_HUMAN161-189290--
1.5ENST000002549425ENSE00000904620chr16:69404532-69404386147TERF2_HUMAN190-238490--
1.6ENST000002549426ENSE00000904618chr16:69402385-69402279107TERF2_HUMAN239-274360--
1.7ENST000002549427ENSE00000904616chr16:69401102-69400710393TERF2_HUMAN274-4051320--
1.8ENST000002549428ENSE00000904614chr16:69395392-6939530786TERF2_HUMAN405-434300--
1.9ENST000002549429ENSE00000904612chr16:69391464-6939142144TERF2_HUMAN434-448150--
1.10ENST0000025494210ENSE00001141451chr16:69390959-693894641496TERF2_HUMAN449-500522A:446-458
B:446-458
13
13

(-) 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:55
 aligned with TERF2_HUMAN | Q15554 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:55
                                   497       507       517       527       537     
          TERF2_HUMAN   488 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLGMN 542
               SCOP domains d3sjma_ A: automated matches                            SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.10    ------------------------------------------ Transcript 1
                 3sjm A 446 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLGMN 500
                                   455       465       475       485       495     

Chain B from PDB  Type:PROTEIN  Length:55
 aligned with TERF2_HUMAN | Q15554 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:55
                                   497       507       517       527       537     
          TERF2_HUMAN   488 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLGMN 542
               SCOP domains d3sjmb_ B: automated matches                            SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.10    ------------------------------------------ Transcript 1
                 3sjm B 446 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLGMN 500
                                   455       465       475       485       495     

Chain C from PDB  Type:DNA  Length:17
                                                 
                 3sjm C   2 TCTAGGGTTAGGGTTAG  18
                                    11       

Chain D from PDB  Type:DNA  Length:17
                                                 
                 3sjm D   2 CTAACCCTAACCCTAGA  18
                                    11       

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TERF2_HUMAN | Q15554)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0098505    G-rich strand telomeric DNA binding    Interacting selectively and non-covalently with G-rich, single-stranded, telomere-associated DNA.
    GO:0003691    double-stranded telomeric DNA binding    Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
    GO:0044877    macromolecular complex binding    Interacting selectively and non-covalently with any macromolecular complex.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003720    telomerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence.
    GO:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
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:0090398    cellular senescence    A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
    GO:1903770    negative regulation of beta-galactosidase activity    Any process that stops, prevents or reduces the frequency, rate or extent of beta-galactosidase activity.
    GO:2000773    negative regulation of cellular senescence    Any process that stops, prevents or reduces the frequency, rate or extent of cellular senescence.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1904430    negative regulation of t-circle formation    Any process that stops, prevents or reduces the frequency, rate or extent of t-circle formation.
    GO:1904354    negative regulation of telomere capping    Any process that stops, prevents or reduces the frequency, rate or extent of telomere capping.
    GO:0032205    negative regulation of telomere maintenance    Any process that stops, prevents, or reduces the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0032208    negative regulation of telomere maintenance via recombination    Any process that stops, prevents, or reduces the frequency, rate or extent of a recombinational process involved in the maintenance of proper telomeric length.
    GO:0032214    negative regulation of telomere maintenance via semi-conservative replication    Any process that stops, prevents, or reduces the frequency, rate or extent of the semi-conservative replication of telomeric DNA.
    GO:1903824    negative regulation of telomere single strand break repair    Any process that stops, prevents or reduces the frequency, rate or extent of telomere single strand break repair.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0051000    positive regulation of nitric-oxide synthase activity    Any process that activates or increases the activity of the enzyme nitric-oxide synthase.
    GO:0032206    positive regulation of telomere maintenance    Any process that activates or increases the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0031848    protection from non-homologous end joining at telomere    A process that prevents non-homologous end joining at telomere, thereby ensuring that telomeres do not fuse.
    GO:0070198    protein localization to chromosome, telomeric region    Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome.
    GO:0032204    regulation of telomere maintenance    Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0032210    regulation of telomere maintenance via telomerase    Any process that modulates the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    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.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0007004    telomere maintenance via telomerase    The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.
    GO:0031627    telomeric loop formation    The process in which linear telomeric DNA is remodeled into duplex loops, by the invasion of a 3' single-stranded overhang into the duplex region.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030870    Mre11 complex    Trimeric protein complex that possesses endonuclease activity; involved in meiotic recombination, DNA repair and checkpoint signaling. In Saccharomyces cerevisiae, the complex comprises Mre11p, Rad50p, and Xrs2p; complexes identified in other species generally contain proteins orthologous to the Saccharomyces cerevisiae proteins.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000783    nuclear telomere cap complex    A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0070187    shelterin complex    A nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex is known to contain TERF1, TERF2, POT1, RAP1, TINF2 and ACD in mammalian cells, and Pot1, Tpz1, Rap1, Rif1, Rif2 and Taz1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1, which acts as an effector molecule along with Ccq1.

 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 3sjm)
 
  Sites
(no "Sites" information available for 3sjm)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3sjm)
 

(-) 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
  3sjm
    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
  TERF2_HUMAN | Q15554
    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
  TERF2_HUMAN | Q15554
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TERF2_HUMAN | Q155541h6p 1vf9 1vfc 1w0u 1xg1 3bu8 3bua 3k6g 4m7c 4rqi 5wqd

(-) Related Entries Specified in the PDB File

1vfc 1w0u