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(-) Description

Title :  MOUSE LIN28A IN COMPLEX WITH LET-7F-1 MICRORNA PRE-ELEMENT
 
Authors :  Y. Nam, P. Sliz
Date :  11 Sep 11  (Deposition) - 16 Nov 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym./Biol. Unit :  A,B,U,V
Keywords :  Microrna Biogenesis, Protein-Rna Complex, Pre-Element, Cchc Zinc Knuckle, Cold Shock Domain, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Nam, C. Chen, R. I. Gregory, J. J. Chou, P. Sliz
Molecular Basis For Interaction Of Let-7 Micrornas With Lin28.
Cell(Cambridge, Mass. ) V. 147 1080 2011
PubMed-ID: 22078496  |  Reference-DOI: 10.1016/J.CELL.2011.10.020

(-) Compounds

Molecule 1 - PROTEIN LIN-28 HOMOLOG A
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLIN28, LIN28A, TEX17
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymLIN-28A, TESTIS-EXPRESSED PROTEIN 17
 
Molecule 2 - RNA (5'- R(*GP*GP*GP*GP*UP*AP*GP*UP*GP*AP*UP*UP*UP*UP*AP*CP*CP*CP*UP*GP*GP*AP* G)-3')
    ChainsU, V
    EngineeredYES
    Other DetailsPREE-LET-7F-1
    Other Details - SourceRNA OLIGONUCLEOTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABUV

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GMP2Mod. NucleotideGUANOSINE
2ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:139 , CYS A:142 , HIS A:147 , CYS A:152BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARECYS A:161 , CYS A:164 , HIS A:169 , CYS A:174BINDING SITE FOR RESIDUE ZN A 201
3AC3SOFTWARECYS B:139 , CYS B:142 , HIS B:147 , CYS B:152BINDING SITE FOR RESIDUE ZN B 200
4AC4SOFTWARECYS B:161 , CYS B:164 , HIS B:169 , CYS B:174BINDING SITE FOR RESIDUE ZN B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TS0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:67 -Pro A:68
2Asp B:67 -Pro B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TS0)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CCHCPS50158 Zinc finger CCHC-type profile.LN28A_MOUSE138-153
 
  2A:138-153
B:138-153

(-) Exons   (0, 0)

(no "Exon" information available for 3TS0)

(-) Sequences/Alignments

Asymmetric/Biological 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:136
 aligned with LN28A_MOUSE | Q8K3Y3 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:145
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174     
          LN28A_MOUSE    35 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKGKNMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee.hhh............eeeeeeeee..eeeeeeeehhhhh...........---------..................................hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------ZF_CCHC         -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ts0 A  35 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKG---------GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ 179
                                    44        54        64        74        84        94       104       114       124 |       - |     144       154       164       174     
                                                                                                                     126       136                                           

Chain B from PDB  Type:PROTEIN  Length:136
 aligned with LN28A_MOUSE | Q8K3Y3 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:145
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174     
          LN28A_MOUSE    35 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKGKNMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee.hhh............eeeeeeeee..eeeeeeeehhhhh...........---------..................................hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------ZF_CCHC         -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ts0 B  35 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKG---------GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ 179
                                    44        54        64        74        84        94       104       114       124 |       - |     144       154       164       174     
                                                                                                                     126       136                                           

Chain U from PDB  Type:RNA  Length:23
                                                       
                 3ts0 U   1 xGGGUAGUGAUUUUACCCUGGAG  23
                            |       10        20   
                            1-GMP                  

Chain V from PDB  Type:RNA  Length:23
                                                       
                 3ts0 V   1 xGGGUAGUGAUUUUACCCUGGAG  23
                            |       10        20   
                            1-GMP                  

   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  (0, 0)

(no "SCOP Domain" information available for 3TS0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TS0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TS0)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LN28A_MOUSE | Q8K3Y3)
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:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035198    miRNA binding    Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0031369    translation initiation factor binding    Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
    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:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    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:0010586    miRNA metabolic process    The chemical reactions and pathways involving miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression.
    GO:0045686    negative regulation of glial cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation.
    GO:1901724    positive regulation of cell proliferation involved in kidney development    Any process that activates or increases the frequency, rate or extent of cell proliferation involved in kidney development.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0045727    positive regulation of translation    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0031054    pre-miRNA processing    Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
    GO:0060964    regulation of gene silencing by miRNA    Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048863    stem cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    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

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

UniProtKB/Swiss-Prot
        LN28A_MOUSE | Q8K3Y33trz 3ts2

(-) Related Entries Specified in the PDB File

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