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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGTG
 
Authors :  D. L. Theobald, S. C. Schultz
Date :  29 May 03  (Deposition) - 17 Jun 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,D,G,H
Keywords :  Single Strand Dna Binding Protein, Protein Dna Interactions, Sequence Specificity, Noncognate, Oligonucleotide And Oligosaccharide Binding Fold, Ob Fold, Telomeres, Protein/Dna, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Theobald, S. C. Schultz
Nucleotide Shuffling And Ssdna Recognition In Oxytricha Nov Telomere End-Binding Protein Complexes
Embo J. V. 22 4314 2003
PubMed-ID: 12912928  |  Reference-DOI: 10.1093/EMBOJ/CDG415

(-) Compounds

Molecule 1 - 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'
    Chains: G, H
    Engineered: YES
    Other Details: CHAINS G AND H ARE A G-QUARTET LINKED DNA DIMER. 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES.
    Synthetic: YES
 
Molecule 2 - 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*TP*G)-3'
    Chains: D
    Engineered: YES
    Other Details: CHAIN D IS SINGLE STRAND DNA. 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES, G TO T SUBSTITUTION.
    Synthetic: YES
 
Molecule 3 - TELOMERE-BINDING PROTEIN ALPHA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKT7
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAC-56A AND MAC-56K AND MAC-56S
    Organism Scientific: STERKIELLA NOVA
    Organism Taxid: 200597
    Other Details: ALANINE VERSION
    Synonym: TELOMERE-BINDING PROTEIN 56 KDA SUBUNIT, TEBP ALPHA
 
Molecule 4 - TELOMERE-BINDING PROTEIN BETA SUBUNIT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKT7
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 9-224
    Gene: MAC-41A AND MAC-41S
    Organism Scientific: STERKIELLA NOVA
    Organism Taxid: 200597
    Synonym: TELOMERE-BINDING PROTEIN 41 KDA SUBUNIT, TEBP BETA

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABDGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NA4Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG G:4 , DT G:5 , DT G:7 , DG G:9 , HOH G:500 , DG H:1 , DG H:12BINDING SITE FOR RESIDUE NA G 1001
2AC2SOFTWAREDG G:2 , DG G:3 , DG G:9 , DG G:10 , DG H:1 , DG H:2 , DG H:11BINDING SITE FOR RESIDUE NA H 1002
3AC3SOFTWAREDG G:1 , DG G:2 , DG G:11 , DG H:2 , DG H:3 , DG H:10BINDING SITE FOR RESIDUE NA H 1003
4AC4SOFTWAREDG G:1 , DG G:12 , DG H:4 , DT H:5 , DT H:7 , DG H:9 , HOH H:501BINDING SITE FOR RESIDUE NA H 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PH3)

(-) 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 1PH3)

(-) Exons   (0, 0)

(no "Exon" information available for 1PH3)

(-) 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:460
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:460
                                    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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
               SCOP domains d1ph3a1 A:36-204 Telomere end binding protein alpha subunit                                                                                                              d1ph3a2 A:205-328 Telomere end binding protein alpha subunit                                                                d1ph3a3 A:329-495 Telomere end binding protein alpha subunit                                                                                                            SCOP domains
               CATH domains -1ph3A01 A:37-210 Nucleic acid-binding proteins                                                                                                                                1ph3A02 A:211-326 Nucleic acid-binding proteins                                                                     1ph3A03 A:327-495 Nucleic acid-binding proteins                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......eeeeeeeeee...ee.....eeeeeeee..................eeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhh...........ee.........hhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhh...eeeeeeeeeeee....eeeeeee.....eeeeeee...........eeeeeeeee........eeeeeeeeeeeee...hhhhhhhhhhh...hhhhhhhh........ee.eee.hhhh.....hhhhhhhh...hhhhhh..eeeeeeeeeeee..hhhh.eeeee....eeehhhhh....eeeeeeeeeeehhhhh...eeeeeeee...................hhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeee.eee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------E--------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ph3 A  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
                                    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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495


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 d1ph3b_ B: Core domain of telomere end binding protein beta subunit                                                                                                                                                      SCOP domains
               CATH domains 1ph3B00 B:9-224 Telomere-binding Protein Beta Subunit; Chain                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhh..eeeeeeee...eeee...eee.eeehhhhhhhhhhhh...hhhhh...eeeeeeeeeeeee............eeeeeeeeeeee............ee...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.......hhhh.eee........................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ph3 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:12
                                            
                 1ph3 D   1 GGGGTTTTGGTG  12
                                    10  


Chain G from PDB  Type:DNA  Length:12
                                            
                 1ph3 G   1 GGGGTTTTGGGG  12
                                    10  


Chain H from PDB  Type:DNA  Length:12
                                            
                 1ph3 H   1 GGGGTTTTGGGG  12
                                    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  (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 1PH3)

(-) 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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  1ph3
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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 1ph4 1ph5 1ph6 1ph7 1ph8 1ph9 1phj 2i0q
        TEBB_STENO | P16458: 1jb7 1otc 1pa6 1ph1 1ph2 1ph4 1ph5 1ph6 1ph7 1ph8 1ph9 1phj 2i0q

(-) Related Entries Specified in the PDB File

1jb7 SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH COGNATE SSDNA GGGGTTTTGGGG
1k8g 35 KDA N-TERMINAL FRAGMENT OF ALPHA SUBUNIT ALONE COMPLEXED WITH TTGGGG
1kix DIMER OF ALPHA SUBUNIT ALONE COMPLEXED WITH TTTTGGGG
1otc SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH COGNATE SSDNA GGGGTTTTGGGG
1pa6 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG
1ph1 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGGGT
1ph2 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG
1ph4 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGCG
1ph5 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG(3DR)GG
1ph6 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG
1ph7 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGIGG
1ph8 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGCGG
1ph9 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG
1phj CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GG(3DR) GTTTTGGGG