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(-) Description

Title :  THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEXAURIDINE
 
Authors :  F. Mayr, A. Schuetz, N. Doege, U. Heinemann
Date :  05 Mar 12  (Deposition) - 05 Sep 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A (2x),B (2x),C (2x),D (2x),E (2x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Chaperone-Rna Complex, Transcription, Lin-28, Rna, Let-7, Mirna (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 ISOFORM B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: COLD SHOCK DOMAIN, RESIDUES 27-114
    Organism Scientific: XENOPUS TROPICALIS
    Organism Taxid: 8364
 
Molecule 2 - HEXA URIDINE
    Chains: E
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:43 , HOH B:2027 , HIS D:68 , SER D:70 , LYS D:71 , HOH D:2070 , HOH E:2002BINDING SITE FOR RESIDUE GOL B1115
2AC2SOFTWAREPHE B:66 , LYS B:95 , GLU B:98 , HOH B:2119 , HOH B:2126 , TRP D:39 , ASN D:41 , MET D:44 , HOH D:2019 , HOH D:2020 , HOH D:2126 , HOH D:2127BINDING SITE FOR RESIDUE GOL D1114

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ALP)

(-) 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: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 --------------------------------------------------------------------------------------- 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
                 4alp A  27 DPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    36        46        56        66        76        86        96       106       


Chain B from PDB  Type:PROTEIN  Length:86
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:86
                                    38        48        58        68        78        88        98       108      
         B4F6I0_XENTR    29 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
               SCOP domains -------------------------------------------------------------------------------------- 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
                 4alp B  29 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
                                    38        48        58        68        78        88        98       108      


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:86
                                    38        48        58        68        78        88        98       108      
         B4F6I0_XENTR    29 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
               SCOP domains -------------------------------------------------------------------------------------- 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
                 4alp C  29 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
                                    38        48        58        68        78        88        98       108      


Chain D from PDB  Type:PROTEIN  Length:84
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:84
                                    39        49        59        69        79        89        99       109    
         B4F6I0_XENTR    30 VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains ------------------------------------------------------------------------------------ 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
                 4alp D  30 VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    39        49        59        69        79        89        99       109    


Chain E from PDB  Type:RNA  Length:6
                                      
                 4alp E   1 UUUUUU   6
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4ALP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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 Related Entries

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

UniProtKB/TrEMBL
        B4F6I0_XENTR | B4F6I0: 3ulj 4a75 4a76

(-) Related Entries Specified in the PDB File

4a75 THE LIN28 COLD SHOCK DOMAIN ACTS AS AN RNA CHAPERONE
4a76 THE LIN28 COLD SHOCK DOMAIN ACTS AS AN RNA CHAPERONE