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(-) Description

Title :  CRYSTAL STRUCTURE OF APO LIN28B COLD SHOCK DOMAIN
 
Authors :  F. Mayr, A. Schuetz, N. Doege, U. Heinemann
Date :  10 Nov 11  (Deposition) - 15 Aug 12  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.06
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Beta Barrel, Cold Shock Domain Fold, Nucleic Acid Binding, Dna Binding Protein (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 - LIN28B, DNA-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQLINKH
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-114
    Gene: LIN28B
    Organism Common: WESTERN CLAWED FROG
    Organism Scientific: XENOPUS (SILURANA) TROPICALIS
    Organism Taxid: 8364

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (2, 18)
No.NameCountTypeFull Name
1ACT16Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:69 , PHE A:77 , ARG A:78 , HOH A:186 , HOH A:227 , ARG B:32BINDING SITE FOR RESIDUE ACT A 3
2AC2SOFTWAREGOL A:2 , PHE A:97 , GLU B:75 , GLY B:76 , HOH B:134 , HOH B:275BINDING SITE FOR RESIDUE ACT A 4
3AC3SOFTWARELYS A:71 , ARG A:101 , HOH A:185BINDING SITE FOR RESIDUE ACT A 5
4AC4SOFTWAREHIS A:68 , LYS A:71 , HOH A:187 , ACT B:7 , ARG B:43BINDING SITE FOR RESIDUE ACT A 6
5AC5SOFTWAREPHE A:40 , ASN A:41 , VAL A:42 , ARG A:43 , HOH A:194 , HOH A:241 , HOH B:139BINDING SITE FOR RESIDUE ACT A 8
6AC6SOFTWAREACT A:4 , ARG A:54 , LYS A:92 , PHE A:97 , TRP B:39 , ASN B:41 , GLU B:82 , HOH B:134BINDING SITE FOR RESIDUE GOL A 2
7AC7SOFTWARETHR A:52 , SER A:53 , LYS B:92 , SER B:93 , HOH B:190BINDING SITE FOR RESIDUE ACT A 9
8AC8SOFTWAREASN A:41 , ASN B:113 , HOH B:242 , HOH B:278BINDING SITE FOR RESIDUE ACT B 1
9AC9SOFTWAREACT A:6 , PHE A:66 , GLU A:98 , ARG B:43BINDING SITE FOR RESIDUE ACT B 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ULJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ULJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ULJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ULJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3ULJ)

(-) 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
                                    37        47        57        67        77        87        97       107       
         B4F6I0_XENTR    28 PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
               SCOP domains d3ulja_ A: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee.hhh............eeeeeeeee..eeeeeeeehhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3ulj A  28 PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
                                    37        47        57        67        77        87        97       107       


Chain B from PDB  Type:PROTEIN  Length:90
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:106
                                    18        28        38        48        58        68        78        88        98       108      
         B4F6I0_XENTR     9 GTREEQGKLPEQEEEEEEDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
               SCOP domains d3                uljb_ B: automated matches                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------....eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee.hhh............eeeeeeeee..eeeeeeeehhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3ulj B  25 GS----------------DPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 114
                             |       -        28        38        48        58        68        78        88        98       108      
                            26               27
   Legend:   → Mismatch (orange background)
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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 beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ULJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ULJ)

(-) Gene Ontology  (5, 5)

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