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(-) Description

Title :  CRYSTAL STRUCTURE OF POT1 (PROTECTION OF TELOMERE)- SSDNA COMPLEX
 
Authors :  M. Lei, E. R. Podell, P. Baumann, T. R. Cech
Date :  16 Sep 03  (Deposition) - 18 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protrein-Dna Complex, Single-Stranded Telomeric Dna, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lei, E. R. Podell, P. Baumann, T. R. Cech
Dna Self-Recognition In The Structure Of Pot1 Bound To Telomeric Single-Stranded Dna
Nature V. 426 198 2003
PubMed-ID: 14614509  |  Reference-DOI: 10.1038/NATURE02092
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TELOMERIC SINGLE-STRANDED DNA
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - PROTECTION OF TELOMERES PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-185
    Gene: POT1
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TMP1Ligand/IonTHYMIDINE-5'-PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TMP1Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , ARG A:113 , TYR A:115 , GLN A:120 , HOH A:319 , DA C:5BINDING SITE FOR RESIDUE TMP A 280
2AC2SOFTWAREHIS B:86 , ARG B:113 , TYR B:115 , GLN B:120 , HOH B:331 , HOH B:346 , DA D:5BINDING SITE FOR RESIDUE TMP B 281

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QZG)

(-) Sequences/Alignments

Asymmetric 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:170
 aligned with POT1_SCHPO | O13988 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
           POT1_SCHPO     5 VIDSLQLNELLNAGEYKIGELTFQSIRSSQELQKKNTIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGNDLPVIKQVGQPLLLHQITLRSYRDRTQGLSKDQFRYALWPDFSSNSKDTLCPQPMPRLMKTGDKEEQFALLLNKIWDEQTN 174
               SCOP domains d1qzga_ A: Protection of telomeres protein 1, Pot1                                                                                                                         SCOP domains
               CATH domains 1qzgA00 A:5-174 Nucleic acid-binding proteins                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.eeee..eeeehhhhhh......eeeeeeeeeeeeeeeee.......eeeeeeee..........eeeeeee..............eeeeeeeeeeee..eeeeeeeeeeeeee.......................hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qzg A   5 VIDSLQLNELLNAGEYKIGELTFQSIRSSQELQKKNTIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGNDLPVIKQVGQPLLLHQITLRSYRDRTQGLSKDQFRYALWPDFSSNSKDTLCPQPMPRLMKTGDKEEQFALLLNKIWDEQTN 174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with POT1_SCHPO | O13988 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
           POT1_SCHPO     5 VIDSLQLNELLNAGEYKIGELTFQSIRSSQELQKKNTIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGNDLPVIKQVGQPLLLHQITLRSYRDRTQGLSKDQFRYALWPDFSSNSKDTLCPQPMPRLMKTGDKEEQFALLLNKIWDEQTN 174
               SCOP domains d1qzgb_ B: Protection of telomeres protein 1, Pot1                                                                                                                         SCOP domains
               CATH domains 1qzgB00 B:5-174 Nucleic acid-binding proteins                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.eeee..eeeehhhhhh......eeeeeeeeeeeeeeeee.......eeeeeeee..........eeeeeee..............eeeeeeeeeeee..eeeeeeeeeeeeee.......................hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qzg B   5 VIDSLQLNELLNAGEYKIGELTFQSIRSSQELQKKNTIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGNDLPVIKQVGQPLLLHQITLRSYRDRTQGLSKDQFRYALWPDFSSNSKDTLCPQPMPRLMKTGDKEEQFALLLNKIWDEQTN 174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174


Chain C from PDB  Type:DNA  Length:5
                                     
                 1qzg C   1 GGTTA   5


Chain D from PDB  Type:DNA  Length:5
                                     
                 1qzg D   1 GGTTA   5
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POT1_SCHPO | O13988)
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: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.
biological process
    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: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: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.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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.
    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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  1qzg
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 Related Entries

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

UniProtKB/Swiss-Prot
        POT1_SCHPO | O13988: 1qzh 4hid 4hik 4him 4hio 4hj5 4hj7 4hj8 4hj9 4hja

(-) Related Entries Specified in the PDB File

1qzh CRYSTAL STRUCTURE OF POT1 (PROTECTION OF TELOMERE) - SSDNA COMPLEX