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(-) Description

Title :  THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEPTATHYMIDINE
 
Authors :  F. Mayr, A. Schuetz, N. Doege, U. Heinemann
Date :  11 Nov 11  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Chaperone-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Mayr, A. Schutz, N. Doge, U. Heinemann
The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna.
Nucleic Acids Res. V. 40 7492 2012
PubMed-ID: 22570413  |  Reference-DOI: 10.1093/NAR/GKS355

(-) Compounds

Molecule 1 - LIN28 COLD SHOCK DOMAIN
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: WESTERN CLAWED FROG
    Organism Scientific: XENOPUS (SILURANA) TROPICALIS
    Organism Taxid: 8364
 
Molecule 2 - 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'
    Chains: B, D, F, H
    Synonym: HEPTATHYMIDINE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4A76)

(-) Sites  (0, 0)

(no "Site" information available for 4A76)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A76)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A76)

(-) Exons   (0, 0)

(no "Exon" information available for 4A76)

(-) 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 B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:86
                                    37        47        57        67        77        87        97       107      
         B4F6I0_XENTR    28 PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4a76a_ A: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeeeee..eeeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4a76 A  28 PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    37        47        57        67        77        87        97       107      


Chain B from PDB  Type:DNA  Length:7
                                       
                 4a76 B   1 TTTTTTT   7


Chain C from PDB  Type:PROTEIN  Length:85
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:85
                                    38        48        58        68        78        88        98       108     
         B4F6I0_XENTR    29 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4a76c_ C: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeeeee..eeeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4a76 C  29 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    38        48        58        68        78        88        98       108     


Chain D from PDB  Type:DNA  Length:7
                                       
                 4a76 D   1 TTTTTTT   7


Chain E from PDB  Type:PROTEIN  Length:87
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:87
                                    36        46        56        66        76        86        96       106       
         B4F6I0_XENTR    27 DPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4a76e_ E: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee....eeeeeeeee...eeeeeeeeeee................eeeeeeee....eeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4a76 E  27 DPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    36        46        56        66        76        86        96       106       


Chain F from PDB  Type:DNA  Length:4
                                    
                 4a76 F   4 TTTT   7


Chain G from PDB  Type:PROTEIN  Length:88
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:88
                                    35        45        55        65        75        85        95       105        
         B4F6I0_XENTR    26 EDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4a76g_ G: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeeee....eeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4a76 G  26 SDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    35        45        55        65        75        85        95       105        


Chain H from PDB  Type:DNA  Length:5
                                     
                 4a76 H   3 TTTTT   7
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A76)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A76)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (B4F6I0_XENTR | B4F6I0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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  4a76
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 Related Entries

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

UniProtKB/TrEMBL
        B4F6I0_XENTR | B4F6I0: 3ulj 4a75 4alp

(-) Related Entries Specified in the PDB File

4a75 THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEXATHYMIDINE.
4alp THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEXAURIDINE