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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF OXYTRICHA NOVA TELOMERE END BINDING PROTEIN ALPHA SUBUNIT BOTH UNCOMPLEXED AND COMPLEXED WITH TELOMERIC SSDNA
 
Authors :  S. Classen, J. A. Ruggles, S. C. Schultz
Date :  24 Oct 01  (Deposition) - 20 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Protein-Dna Complex, Telomeres, Sequence Specific Ssdna Binding Protein, Ob Folds, Structure, Protein Single Strand Dna Interactions, 3'-Dna End Binding Protein, Telomere End Binding Protein, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Classen, J. A. Ruggles, S. C. Schultz
Crystal Structure Of The N-Terminal Domain Of Oxytricha Nova Telomere End-Binding Protein Alpha Subunit Both Uncomplexed And Complexed With Telomeric Ssdna.
J. Mol. Biol. V. 314 1113 2001
PubMed-ID: 11743727  |  Reference-DOI: 10.1006/JMBI.2000.5191
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(TP*TP*GP*GP*GP*G)-3'
    ChainsD, E
    EngineeredYES
    SyntheticYES
 
Molecule 2 - TELOMERE-BINDING PROTEIN ALPHA SUBUNIT
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKKT7
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL 35KDA SSDNA BINDING DOMAIN
    Organism ScientificSTERKIELLA NOVA
    Organism Taxid200597
    Other DetailsALANINE VERSION
    SynonymALPHA, MACRONUCLEAR ALPHA PROTEIN (ALANINE VERSION), MAC-56A

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)A  D 
Biological Unit 2 (1x) B  E
Biological Unit 3 (1x)  C  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:204 , LYS A:304 , LYS C:216BINDING SITE FOR RESIDUE SO4 A 321
2AC2SOFTWARETYR A:36 , HIS A:123 , ARG A:124 , SER A:145BINDING SITE FOR RESIDUE SO4 A 322
3AC3SOFTWARELYS A:216 , TYR B:203 , SER B:204BINDING SITE FOR RESIDUE SO4 B 321
4AC4SOFTWAREHIS B:123 , ARG B:124 , SER B:176BINDING SITE FOR RESIDUE SO4 B 322
5AC5SOFTWARELYS B:216 , SER C:202 , TYR C:203 , SER C:204 , LYS C:304 , HOH C:362BINDING SITE FOR RESIDUE SO4 C 321
6AC6SOFTWAREHIS C:123 , ARG C:124 , SER C:145 , SER C:176 , HOH C:384BINDING SITE FOR RESIDUE SO4 C 322

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K8G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TEBA_STENO_002 *A311STEBA_STENO  ---  ---A/B/CA311S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TEBA_STENO_002 *A311STEBA_STENO  ---  ---AA311S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TEBA_STENO_002 *A311STEBA_STENO  ---  ---BA311S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TEBA_STENO_002 *A311STEBA_STENO  ---  ---CA311S
   * ID not provided by source

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K8G)

(-) Exons   (0, 0)

(no "Exon" information available for 1K8G)

(-) 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:269
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:280
                                    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       305       315
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQD 315
               SCOP domains d1k8ga1 A:36-204 Telomere end bi    nding protein al       pha subunit                                                                                                   d1k8ga2 A:205-315 Telomere end binding protein alpha subunit                                                    SCOP domains
               CATH domains -1k8gA01 A:37-210 Nucleic acid-b    inding proteins                                                                                                                            1k8gA02 A:211-315 Nucleic acid-binding proteins                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeee......----.eeeeeee........-------...eeeeee..hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhhh..........ee.......hhhhhhhhhhhhhhhhhhhhhh.........hhhhh.....eeeeeeeeeeeee....eeeeeee.....eeeeeee...........eeeeeeee.................eeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8g A  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKT----YICSLKIVDPTLYLKQ-------SDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQD 315
                                    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       305       315
                                                          67   72             87      95                                                                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:281
                                    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       305       315 
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
               SCOP domains d1k8gb1 B:36-204 Telomere end binding protein alpha s      ubunit                                                                                                        d1k8gb2 B:205-316 Telomere end binding protein alpha subunit                                                     SCOP domains
               CATH domains -1k8gB01 B:37-210 Nucleic acid-binding proteins                                                                                                                                1k8gB02 B:211-316 Nucleic acid-binding proteins                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee............eeeeeeeeee...eeee..eeeeeeeee.........------...eeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhhh..........ee.........hhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhh...eeeeeeeeeeeeee..eeeeeee.....eeeeeee...........eeeeeeeee........eee.....eeeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8g B  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQ------SDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
                                    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       305       315 
                                                                               88     95                                                                                                                                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:278
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:281
                                    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       305       315 
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
               SCOP domains d1k8gc1 C:36-204 Telomere end binding protein alpha sub   unit                                                                                                           d1k8gc2 C:205-316 Telomere end binding protein alpha subunit                                                     SCOP domains
               CATH domains 1k8gC01 C:36-210 Nucleic acid-binding proteins                                                                                                                                 1k8gC02 C:211-316 Nucleic acid-binding proteins                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......eeeeeeeeee...eeee..eeeeeeeee...........---....eeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhhh..........ee.......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhh.....eeeeeeeeeeee....eeeeeee.....eeeeeee...........eeeeeee..................eeeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8g C  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKG---ASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
                                    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       305       315 
                                                                                 90  94                                                                                                                                                                                                                              

Chain D from PDB  Type:DNA  Length:4
                                    
                 1k8g D   5 GGGG   8

Chain E from PDB  Type:DNA  Length:4
                                    
                 1k8g E   5 GGGG   8

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K8G)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TEBA_STENO | P295491jb7 1kix 1otc 1pa6 1ph1 1ph2 1ph3 1ph4 1ph5 1ph6 1ph7 1ph8 1ph9 1phj 2i0q

(-) Related Entries Specified in the PDB File

1jb7 DNA G-QUARTETS IN A 1.86 A RESOLUTION STRUCTURE OF AN OXYTRICHA NOVA TELOMERIC PROTEIN-DNA COMPLEX
1otc THE O. NOVA TELOMERE END BINDING PROTEIN COMPLEXED WITH SINGLE STRAND DNA