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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN LIN28B COLD SHOCK DOMAIN
 
Authors :  F. Mayr, A. Schuetz, N. Doege, U. Heinemann
Date :  14 Oct 11  (Deposition) - 08 Aug 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna 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 - PROTEIN LIN-28 HOMOLOG B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQLINKH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PHAGE-RESISTANT
    Expression System Vector Type: PLASMID
    Fragment: COLD SHOCK DOMAIN, RESIDUES 24-111
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LIN28B, LIN-28B

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:90 , SER B:91 , HOH B:2079 , HOH B:2082BINDING SITE FOR RESIDUE GOL B1112
2AC2SOFTWARELYS A:92 , PHE B:37 , ASN B:38 , VAL B:39 , ARG B:40BINDING SITE FOR RESIDUE SO4 B1113

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A4I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A4I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A4I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A4I)

(-) Exons   (0, 0)

(no "Exon" information available for 4A4I)

(-) 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:84
 aligned with LN28B_HUMAN | Q6ZN17 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:84
                                    36        46        56        66        76        86        96       106    
          LN28B_HUMAN    27 VLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTGPGGSPCLGS 110
               SCOP domains d4a4ia_ A: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeee......eeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4a4i A  27 VLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTGPGGSPCLGS 110
                                    36        46        56        66        76        86        96       106    


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with LN28B_HUMAN | Q6ZN17 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:85
                                    36        46        56        66        76        86        96       106     
          LN28B_HUMAN    27 VLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTGPGGSPCLGSE 111
               SCOP domains d4a4ib_ B: 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
                 4a4i B  27 VLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTGPGGSPCLGSE 111
                                    36        46        56        66        76        86        96       106
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A4I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A4I)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LN28B_HUMAN | Q6ZN17)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0031123    RNA 3'-end processing    Any process involved in forming the mature 3' end of an RNA molecule.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0010587    miRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.
    GO:0031054    pre-miRNA processing    Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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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 Related Entries

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(-) Related Entries Specified in the PDB File

4a65 CRYSTAL STRUCTURE OF THE THIOREDOXIN REDUCTASE FROM ENTAMOEBA HISTOLYTICA WITH AUCN
4a76 THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEPTATHYMIDINE
4alp THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEXAURIDINE