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(-) Description

Title :  CRYSTAL STRUCTURE OF A TELOMERE SINGLE-STRAND DNA-PROTEIN COMPLEX FROM O. NOVA WITH FULL-LENGTH ALPHA AND BETA TELOMERE PROTEINS
 
Authors :  M. P. Horvath, P. Buczek
Date :  11 Aug 06  (Deposition) - 22 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Single Strand Dna-Protein Complex, Structural Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Buczek, M. P. Horvath
Structural Reorganization And The Cooperative Binding Of Single-Stranded Telomere Dna In Sterkiella Nova.
J. Biol. Chem. V. 281 40124 2006
PubMed-ID: 17082188  |  Reference-DOI: 10.1074/JBC.M607749200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
    Chains: D
    Engineered: YES
    Other Details: 3'-TERMINAL SINGLE STRAND DNA FRAGMENT FROM OXYTRICHA NOVA (STERKIELLA NOVA) MACRONUCLEAR TELOMERES
    Synthetic: YES
 
Molecule 2 - TELOMERE-BINDING PROTEIN ALPHA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKT7E
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAC-56A
    Organism Scientific: STERKIELLA NOVA
    Organism Taxid: 200597
    Synonym: TELOMERE-BINDING PROTEIN 56 KDA SUBUNIT, TEBP ALPHA
 
Molecule 3 - TELOMERE-BINDING PROTEIN BETA SUBUNIT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKT7E
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAC-41A
    Organism Scientific: STERKIELLA NOVA
    Organism Taxid: 200597
    Synonym: TELOMERE-BINDING PROTEIN 41 KDA SUBUNIT, TEBP BETA

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:157BINDING SITE FOR RESIDUE CL A 496
2AC2SOFTWAREARG A:481 , ASN A:483 , GLY A:484 , LYS B:182 , GLY B:183BINDING SITE FOR RESIDUE CL A 497
3AC3SOFTWAREGLN A:423 , HOH A:635 , GLN B:149 , ARG B:152BINDING SITE FOR RESIDUE CL A 498
4AC4SOFTWARETHR A:126 , ARG A:128 , ASN A:137 , LYS A:447BINDING SITE FOR RESIDUE CL A 499
5AC5SOFTWAREHIS A:234 , GLU A:235 , VAL A:334 , TYR A:474 , HOH A:553 , HOH A:615BINDING SITE FOR RESIDUE EDO A 500
6AC6SOFTWARESER A:208 , TYR A:211 , HOH A:647 , HOH A:702BINDING SITE FOR RESIDUE EDO A 501
7AC7SOFTWARETHR A:82 , LEU A:83 , TYR A:84 , LEU A:85 , ASP A:96BINDING SITE FOR RESIDUE EDO A 502
8AC8SOFTWAREGLU A:379 , PRO A:380 , SER A:381 , GLY B:166 , ASP B:167 , ASN B:168BINDING SITE FOR RESIDUE EDO B 386
9AC9SOFTWAREARG A:370 , GLN A:372BINDING SITE FOR RESIDUE EDO A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I0Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:379 -Pro A:380
2Tyr B:47 -Pro B:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TEBB_STENO_001 *A110STEBB_STENO  ---  ---BA110S
2UniProtVAR_TEBA_STENO_002 *A311STEBA_STENO  ---  ---AA311S
3UniProtVAR_TEBA_STENO_003 *D456ETEBA_STENO  ---  ---AD456E
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2I0Q)

(-) 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:461
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:461
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494 
           TEBA_STENO    35 KYEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
               SCOP domains d2i0qa1 A:35-204 Telomere end binding protein alpha subunit                                                                                                               d2i0qa2 A:205-328 Telomere end binding protein alpha subunit                                                                d2i0qa3 A:329-495 Telomere end binding protein alpha subunit                                                                                                            SCOP domains
               CATH domains --2i0qA01 A:37-210 Nucleic acid-binding proteins                                                                                                                                2i0qA02 A:211-326 Nucleic acid-binding proteins                                                                     2i0qA03 A:327-495 Nucleic acid-binding proteins                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeee...eeee..eeeeeeeee..................eeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhh...........ee..........hhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhh...eeeeeeeeeeee....eeeeeee.....eeeeeee...........eeeeeeeee........eeeeeeeeeeeee...hhhhhhhhhhh...hhhhhhhh........ee.eee.hhhh.....hhhhhhhh...hhhhhh..eeeeeeeeeeee..hhhh.eeeee....eee.........eeeeeeeeeeehhhhh...eeeeeeee...................hhhhhhhhhhhhhhhh...eeeeeeeeee..eeeee.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------E--------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i0q A  35 KYEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494 


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with TEBB_STENO | P16458 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:216
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
           TEBB_STENO     9 QQQSAFKQLYTELFNNEGDFSKVSSNLKKPLKCYVKESYPHFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIVINNWSLELRRVNSAEVFTSYANLEARLIVHSFKPNLQERLNPTRYPVNLFRDDEFKTTIQHFRHTALQAAINKTVKGDNLVDISKVADAAGKKGKVDAGIVKASASKGDEFSDFSFKEGNTATLKIADIFVQEKG 224
               SCOP domains d2i0qb1 B:9-224 Core domain of telomere end binding protein beta subunit                                                                                                                                                 SCOP domains
               CATH domains 2i0qB00 B:9-224 Telomere-binding Protein Beta Subunit; Chain                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhh..eeeeeeee...eeee...eee.eeehhhhhhhhhh.....hhhhh...eeeeeeeeeeeee............eeeeeeeeeeee............ee...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhh.eee......................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i0q B   9 QQQSAFKQLYTELFNNEGDFSKVSSNLKKPLKCYVKESYPHFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIVINNWSLELRRVNSAEVFTSYANLEARLIVHSFKPNLQERLNPTRYPVNLFRDDEFKTTIQHFRHTALQAAINKTVKGDNLVDISKVADAAGKKGKVDAGIVKASASKGDEFSDFSFKEGNTATLKIADIFVQEKG 224
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      


Chain D from PDB  Type:DNA  Length:11
                                           
                 2i0q D   6 GGGTTTTGGGG  16
                                    15
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I0Q)

(-) Gene Ontology  (9, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TEBA_STENO | P29549)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043047    single-stranded telomeric DNA binding    Interacting selectively and non-covalently with single-stranded telomere-associated DNA.
biological process
    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:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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.

Chain B   (TEBB_STENO | P16458)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
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: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.

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  2i0q
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  TEBA_STENO | P29549
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  TEBB_STENO | P16458
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 Related Entries

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

UniProtKB/Swiss-Prot
        TEBA_STENO | P29549: 1jb7 1k8g 1kix 1otc 1pa6 1ph1 1ph2 1ph3 1ph4 1ph5 1ph6 1ph7 1ph8 1ph9 1phj
        TEBB_STENO | P16458: 1jb7 1otc 1pa6 1ph1 1ph2 1ph3 1ph4 1ph5 1ph6 1ph7 1ph8 1ph9 1phj

(-) Related Entries Specified in the PDB File

1jb7 SAME TELOMERE COMPLEX WITH D(GGGGTTTTGGGG) SSDNA CRYSTALIZED UNDER LOW SALT CONDITIONS; 1.86 A RESOLUTION
1otc SAME TELOMERE COMPLEX WITH D(GGGGTTTTGGGG) SSDNA CRYSTALIZED UNDER LOW SALT CONDITIONS; 2.8 A RESOLUTION