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(-) Description

Title :  HTRF1 DNA-BINDING DOMAIN IN COMPLEX WITH TELOMERIC DNA.
 
Authors :  R. I. Court, L. M. Chapman, L. Fairall, D. Rhodes
Date :  11 Jun 04  (Deposition) - 22 Dec 04  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Telomere, Dna-Binding Protein, Homeodomain, Mitosis, Cell Cycle, Nuclear Protein, Chromosomal Protein, Phosphorylation, Adp-Ribosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. I. Court, L. M. Chapman, L. Fairall, D. Rhodes
How The Human Telomeric Proteins Trf1 And Trf2 Recognize Telomeric Dna: A View From High-Resolution Crystal Structures
Embo Rep. V. 6 39 2005
PubMed-ID: 15608617  |  Reference-DOI: 10.1038/SJ.EMBOR.7400314

(-) Compounds

Molecule 1 - TELOMERIC REPEAT BINDING FACTOR 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET13A
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Fragment: DNA-BINDING DOMAIN, RESIDUES 379-431
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHETIC GENE
    Synonym: TTAGGG REPEAT-BINDING FACTOR 1, NIMA- INTERACTING PROTEIN 2, TELOMERIC PROTEIN PIN2/TRF1
 
Molecule 2 - 5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP *TP*AP*GP*GP*GP*TP*TP*AP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP *AP*CP*CP*CP*TP*AP*AP*CP*A)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES

 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 1W0T)

(-) Sites  (0, 0)

(no "Site" information available for 1W0T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W0T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W0T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W0T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W0T)

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002766031aENSE00001408652chr8:73921099-73921440342TERF1_HUMAN1-1071070--
1.3ENST000002766033ENSE00000980813chr8:73926130-7392622596TERF1_HUMAN107-139330--
1.4ENST000002766034ENSE00000980814chr8:73932919-73933040122TERF1_HUMAN139-179410--
1.5bENST000002766035bENSE00000980815chr8:73934451-7393453787TERF1_HUMAN180-208290--
1.6ENST000002766036ENSE00000980816chr8:73937057-73937206150TERF1_HUMAN209-258500--
1.7bENST000002766037bENSE00000980817chr8:73939175-73939287113TERF1_HUMAN259-296380--
1.8bENST000002766038bENSE00000980818chr8:73942571-7394263060TERF1_HUMAN296-316210--
1.8dENST000002766038dENSE00000980819chr8:73944277-7394436892TERF1_HUMAN316-347320--
1.10ENST0000027660310ENSE00001087264chr8:73951351-73951454104TERF1_HUMAN347-381352A:379-381
B:379-381		3
3
1.11aENST0000027660311aENSE00002096154chr8:73958196-73958706511TERF1_HUMAN382-439582A:382-430
B:382-430		49
49

(-) 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:52
 aligned with TERF1_HUMAN | P54274 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:52
                                   388       398       408       418       428  
          TERF1_HUMAN   379 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKL 430
               SCOP domains d1w0ta_ A:                                           SCOP domains
               CATH domains 1w0tA00 A:379-430 Homeodomain-like                   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
               Transcript 1 1.1Exon 1.11a  PDB: A:382-430 UniProt: 382-439       Transcript 1
                 1w0t A 379 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKL 430
                                   388       398       408       418       428  


Chain B from PDB  Type:PROTEIN  Length:52
 aligned with TERF1_HUMAN | P54274 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:52
                                   388       398       408       418       428  
          TERF1_HUMAN   379 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKL 430
               SCOP domains d1w0tb_ B:                                           SCOP domains
               CATH domains 1w0tB00 B:379-430 Homeodomain-like                   CATH domains
           Pfam domains (1) -Myb_DNA-binding-1w0tB01 B:380-428                -- Pfam domains (1)
           Pfam domains (2) -Myb_DNA-binding-1w0tB02 B:380-428                -- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
               Transcript 1 1.1Exon 1.11a  PDB: B:382-430 UniProt: 382-439       Transcript 1
                 1w0t B 379 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKL 430
                                   388       398       408       418       428  


Chain C from PDB  Type:DNA  Length:19
                                                   
                 1w0t C   1 CTGTTAGGGTTAGGGTTAG  19
                                    10         


Chain D from PDB  Type:DNA  Length:19
                                                   
                 1w0t D   1 TCTAACCCTAACCCTAACA  19
                                    10
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TERF1_HUMAN | P54274)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    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:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    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:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0045141    meiotic telomere clustering    The cell cycle process in which the dynamic reorganization of telomeres occurs in early meiotic prophase, during which meiotic chromosome ends are gathered in a bouquet arrangement at the inner surface of the nuclear envelope proximal to the spindle pole body. This plays an important role in progression through meiosis and precedes synapsis.
    GO:0007094    mitotic spindle assembly checkpoint    A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:1904911    negative regulation of establishment of RNA localization to telomere    Any process that stops, prevents or reduces the frequency, rate or extent of establishment of RNA localization to telomere.
    GO:1904914    negative regulation of establishment of macromolecular complex localization to telomere    Any process that stops, prevents or reduces the frequency, rate or extent of establishment of macromolecular complex localization to telomere.
    GO:1904850    negative regulation of establishment of protein localization to telomere    Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization to telomere.
    GO:0051974    negative regulation of telomerase activity    Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    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:0032211    negative regulation of telomere maintenance via telomerase    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0031116    positive regulation of microtubule polymerization    Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
    GO:0045931    positive regulation of mitotic cell cycle    Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
    GO:1904792    positive regulation of shelterin complex assembly    Any process that activates or increases the frequency, rate or extent of shelterin complex assembly.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    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: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: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.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TERF1_HUMAN | P54274: 1ba5 1h6o 1ity 1iv6 3bqo 3l82 5hkp

(-) Related Entries Specified in the PDB File

1ba5 DNA-BINDING DOMAIN OF HUMAN TELOMERIC PROTEIN, HTRF1,NMR, 18 STRUCTURES
1h6o DIMERISATION DOMAIN FROM HUMAN TRF1
1ity SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF HUMAN TRF1
1iv6 SOLUTION STRUCTURE OF THE DNA COMPLEX OF HUMAN TRF1
1w0u HTRF2 DNA-BINDING DOMAIN IN COMPLEX WITH TELOMERIC DNA