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(-) Description

Title :  CRYSTAL STRUCTURE OF NGTRF COMPLEXED WITH TELOMERIC DNA
 
Authors :  H. -S. Cho, J. -S. Byun, S. -H. Jun
Date :  02 Jul 07  (Deposition) - 15 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  B,C,D  (1x)
Biol. Unit 2:  A,E,F  (1x)
Keywords :  Plant, Protein-Dna Complex, Double Helix, Telomere Binding Protein, Ngtrf, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -S. Cho, J. -S. Byun, S. -H. Jun, W. Han, W. Lee
Complex Structure Of Plant Telomere Bindig Protein, Ngtrf And Telomere Dna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TELOMERE BINDING PROTEIN TBP1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: BL21 (DE3)
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 574-659
    Gene: NGTRF
    Organism Common: TOBACCO
    Organism Scientific: NICOTIANA GLUTINOSA
 
Molecule 2 - 5'-D(P*TP*TP*TP*AP*GP*GP*G)-3'
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(P*CP*CP*CP*TP*AP*AP*A)-3'
    Chains: D, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x):  BCD  
Biological Unit 2 (1x): A   EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2QHB)

(-) Sites  (0, 0)

(no "Site" information available for 2QHB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QHB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QHB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QHB)

(-) 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:86
 aligned with Q84ZU4_NICGU | Q84ZU4 from UniProtKB/TrEMBL  Length:681

    Alignment length:86
                                   583       593       603       613       623       633       643       653      
         Q84ZU4_NICGU   574 RRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAYWSQ 659
               SCOP domains d2qhba_ A: Telomere binding protein TBP1                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2qhb A 574 RRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAYWSQ 659
                                   583       593       603       613       623       633       643       653      


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with Q84ZU4_NICGU | Q84ZU4 from UniProtKB/TrEMBL  Length:681

    Alignment length:85
                                   584       594       604       614       624       634       644       654     
         Q84ZU4_NICGU   575 RIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAYWSQ 659
               SCOP domains d2qhbb_ B: Telomere binding protein TBP1                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2qhb B 575 RIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAYWSQ 659
                                   584       594       604       614       624       634       644       654     


Chain C from PDB  Type:DNA  Length:7
                                       
                 2qhb C   1 TTTAGGG   7


Chain D from PDB  Type:DNA  Length:7
                                       
                 2qhb D   8 CCCTAAA  14


Chain E from PDB  Type:DNA  Length:7
                                       
                 2qhb E   1 TTTAGGG   7


Chain F from PDB  Type:DNA  Length:7
                                       
                 2qhb F   8 CCCTAAA  14
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  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 alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QHB)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q84ZU4_NICGU | Q84ZU4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q84ZU4_NICGU | Q84ZU4: 2ckx
UniProtKB/TrEMBL
        Q84ZU4_NICGU | Q84ZU4: 2juh

(-) Related Entries Specified in the PDB File

2ckx CRYSTAL STRUCTURE OF NGTRF