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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN POT1 BOUND TO TELOMERIC SINGLE-STRANDED DNA (TTAGGGTTAG)
 
Authors :  M. Lei, E. R. Podell, T. R. Cech
Date :  25 Sep 04  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Telomere; Protein-Dna Complex; Single-Stranded Dna, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Lei, E. R. Podell, T. R. Cech
Structure Of Human Pot1 Bound To Telomeric Single-Stranded Dna Provides A Model For Chromosome End-Protection
Nat. Struct. Mol. Biol. V. 11 1223 2004
PubMed-ID: 15558049  |  Reference-DOI: 10.1038/NSMB867
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HT10 D(TTAGGGTTAG)
    ChainsB
    EngineeredYES
    Other DetailsSINGLE-STRANDED DNA
    Other Details - SourceTHIS SEQUENCE OCCURS NATURALLY IN HUMANS
    SyntheticYES
 
Molecule 2 - PROTECTION OF TELOMERES 1
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBAC
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACMID
    FragmentSPLICING VARIANT 2 (HPOT1V2)
    GenePOT1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 1XJV)

(-) Sites  (0, 0)

(no "Site" information available for 1XJV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric/Biological Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071390Y89CPOTE1_HUMANDisease (CMM10)587777472AY89C
2UniProtVAR_071391Q94EPOTE1_HUMANDisease (CMM10)587777474AQ94E
3UniProtVAR_075717G95CPOTE1_HUMANDisease (GLM9)797045168AG95C
4UniProtVAR_071392R137HPOTE1_HUMANDisease (CMM10)587777475AR137H
5UniProtVAR_071393D224NPOTE1_HUMANDisease (CMM10)202187871AD224N
6UniProtVAR_071394S270NPOTE1_HUMANDisease (CMM10)587777477AS270N
7UniProtVAR_071395R273LPOTE1_HUMANDisease (CMM10)587777476AR273L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003576281bENSE00001894981chr7:124570035-124569848188POTE1_HUMAN-00--
1.2bENST000003576282bENSE00001405298chr7:124569053-124568869185POTE1_HUMAN-00--
1.3ENST000003576283ENSE00001404825chr7:124555700-12455562873POTE1_HUMAN-00--
1.4ENST000003576284ENSE00001401958chr7:124538428-124538315114POTE1_HUMAN-00--
1.6aENST000003576286aENSE00002191404chr7:124537266-12453721948POTE1_HUMAN1-330--
1.8ENST000003576288ENSE00001623568chr7:124532434-124532320115POTE1_HUMAN4-42391A:6-4237
1.9bENST000003576289bENSE00001785664chr7:124511095-124510965131POTE1_HUMAN42-85441A:42-8544
1.10aENST0000035762810aENSE00001732194chr7:124503694-124503404291POTE1_HUMAN86-182971A:86-182 (gaps)97
1.11bENST0000035762811bENSE00001136138chr7:124499166-124499011156POTE1_HUMAN183-234521A:183-23452
1.12ENST0000035762812ENSE00001136133chr7:124493192-124493026167POTE1_HUMAN235-290561A:235-29056
1.13ENST0000035762813ENSE00001136130chr7:124492005-12449192680POTE1_HUMAN290-317281A:290-29910
1.15ENST0000035762815ENSE00001611896chr7:124487052-12448699657POTE1_HUMAN317-336200--
1.16bENST0000035762816bENSE00001701311chr7:124483017-124482861157POTE1_HUMAN336-388530--
1.17bENST0000035762817bENSE00001715885chr7:124481232-124481027206POTE1_HUMAN388-457700--
1.18ENST0000035762818ENSE00001685271chr7:124475468-124475333136POTE1_HUMAN457-502460--
1.19ENST0000035762819ENSE00001773174chr7:124469396-12446930889POTE1_HUMAN502-532310--
1.21aENST0000035762821aENSE00001618916chr7:124467359-12446726892POTE1_HUMAN532-562310--
1.22ENST0000035762822ENSE00001688617chr7:124465411-124465306106POTE1_HUMAN563-598360--
1.23eENST0000035762823eENSE00001863642chr7:124464128-1244624401689POTE1_HUMAN598-634370--

(-) 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:291
 aligned with POTE1_HUMAN | Q9NUX5 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:294
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    
          POTE1_HUMAN     6 ATNYIYTPLNQLKGGTIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYEALPIIYKNGDIVRFHRLKIQVYKKETQGITSSGFASLTFEGTLGAPIIPRTSSKYFNFTTEDHKMVEALRVWASTHMSPSWTLLKLCDVQPMQYFDLTCQLLGKAEVDGASFLLKVWDGTRTPFPSWRVLIQDLVLEGDLSHIHRLQNLTIDILVYDNHVHVARSLKVGSFLRIYSLHTKLQSMNSENQTMLSLEFHLHGGTSYGRGIRVLPESNSDVDQLKKDLESANLTA 299
               SCOP domains d1xjva1 A:6-145 Protection of telomeres protein 1, Pot1                                                                                     ---d1xjva2 A:149-299 Protection of telomeres protein 1, Pot1                                                                                               SCOP domains
               CATH domains 1xjvA01 A:6-150 Nucleic acid-binding proteins                                                                                                    1xjvA02 A:151-299 Protection of telomeres; domain 2                                                                                                   CATH domains
               Pfam domains -----Telo_bind-1xjvA01 A:11-141                                                                                                         -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...eeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeee.hhhhh........eeeeeeeeeeee..eeeeeeeeeeeeeee...................hhhhhhhhhhhhhhhhhhh.---...hhhhh....eeeeeeeeeeeee....eeeeeee...................eehhhhhhhhhhhheeeeee.hhhhhhhhh....eeeeeeeeeeeeee.....eeeeeeeee...hhhhheeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------C----EC-----------------------------------------H--------------------------------------------------------------------------------------N---------------------------------------------N--L-------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.8  PDB: A:6-42 UniProt: 4-42  -------------------------------------------Exon 1.10a  PDB: A:86-182 (gaps) UniProt: 86-182                                                 Exon 1.11b  PDB: A:183-234 UniProt: 183-234         Exon 1.12  PDB: A:235-290 UniProt: 235-290              --------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.9b  PDB: A:42-85 UniProt: 42-85      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13  Transcript 1 (2)
                 1xjv A   6 ATNYIYTPLNQLKGGTIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYEALPIIYKNGDIVRFHRLKIQVYKKETQGITSSGFASLTFEGTLGAPIIPRTSSKYFNFTTEDHKMVEALRVWASTHMS---TLLKLCDVQPMQYFDLTCQLLGKAEVDGASFLLKVWDGTRTPFPSWRVLIQDLVLEGDLSHIHRLQNLTIDILVYDNHVHVARSLKVGSFLRIYSLHTKLQSMNSENQTMLSLEFHLHGGTSYGRGIRVLPESNSDVDQLKKDLESANLTA 299
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145   |   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    
                                                                                                                                                                     145 149                                                                                                                                                      

Chain B from PDB  Type:DNA  Length:10
                                          
                 1xjv B   1 TTAGGGTTAG  10
                                    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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (POTE1_HUMAN | Q9NUX5)
molecular function
    GO:0017151    DEAD/H-box RNA helicase binding    Interacting selectively and non-covalently with the enzyme DEAD/H-box RNA helicase.
    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: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.
    GO:0010521    telomerase inhibitor activity    Stops, prevents or reduces the activity of a telomerase. Telomerase catalyzes 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:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0070200    establishment of protein localization to telomere    The directed movement of a protein to a specific location in the telomeric region of a chromosome.
    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:0060383    positive regulation of DNA strand elongation    Any process that increases the rate, frequency or extent of DNA strand elongation. DNA strand elongation is the DNA metabolic process in which a DNA strand is synthesized by adding nucleotides to the 3' end of an existing DNA stand.
    GO:0051096    positive regulation of helicase activity    Any process that activates or increases the activity of a helicase.
    GO:0051973    positive regulation of telomerase activity    Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0032202    telomere assembly    A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a telomere at a non-telomeric double-stranded DNA end. A telomere is a terminal region of a linear chromosome that includes telomeric DNA repeats and associated proteins.
    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.
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POTE1_HUMAN | Q9NUX53kjo 3kjp 5h65 5un7

(-) Related Entries Specified in the PDB File

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