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(-) Description

Title :  ZIPCODE-BINDING-PROTEIN-1 KH3KH4(DD) DOMAINS IN COMPLEX WITH THE KH3 RNA TARGET
 
Authors :  G. Nicastro, A. M. Candel, A. Ramos, D. Hollingworth
Date :  21 Oct 15  (Deposition) - 25 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (12x)
NMR Structure *:  A,B  (1x)
Keywords :  Kh Domain, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Nicastro, A. M. Candel, A. Ramos, D. Hollingworth
Zipcode-Binding-Protein-1 Kh3Kh4(Dd) Domains In Complex Wit The Rna Target Gcacaccc
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INSULIN-LIKE GROWTH FACTOR 2 MRNA-BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentKH DOMAIN (UNP RESIDUES 387-573)
    GeneIGF2BP1, VICKZ1, ZBP1
    MutationYES
    Organism CommonBANTAM,CHICKENS
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymIGF2 MRNA-BINDING PROTEIN 1, IMP-1, IGF-II MRNA-BINDING PROTEIN 1, VICKZ FAMILY MEMBER 1, ZIP-CODE BINDING POLYPEPTIDE, ZIPCODE-BINDING PROTEIN 1, ZBP-1
 
Molecule 2 - RNA (5'-R(P*GP*CP*AP*CP*AP*CP*CP*C)-3')
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (12x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2N8L)

(-) Sites  (0, 0)

(no "Site" information available for 2N8L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2N8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2N8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2N8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2N8L)

(-) Exons   (0, 0)

(no "Exon" information available for 2N8L)

(-) Sequences/Alignments

NMR Structure
   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:191
 aligned with IF2B1_CHICK | O42254 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:203
                                   380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570   
          IF2B1_CHICK   371 AAVGLFPASSNAVPPPPSSVSGAAPYSSFMPPEQETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVVITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENEQVIVKIIGHFYASQMAQRKIRDILAQVKQQHQKGQSGQLQA 573
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....------------..................eeeeeeeehhhhhhhhhhhhhhhhhhhhhhh.eeee.........eeeeeeeehhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhh....hhhhhhhhhhh.eee......hhhh.eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2n8l A   1 GAMG------------PSSVSGAAPFSSFMPPEQETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVVITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGDDGKTVNELQNLTAAEVVVPRDQTPDENEQVIVKIIGHFYASQMAQRKIRDILAQVKQQHQKGQSGQLQA 191
                               |     -      |  8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   
                               4            5                                                                                                                                                                                          

Chain B from PDB  Type:RNA  Length:8
                                        
                 2n8l B   1 GCACACCC   8

   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 2N8L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2N8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2N8L)

(-) Gene Ontology  (26, 26)

NMR Structure(hide GO term definitions)
Chain A   (IF2B1_CHICK | O42254)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0048027    mRNA 5'-UTR binding    Interacting selectively and non-covalently with the 5' untranslated region of an mRNA molecule.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0045182    translation regulator activity    Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
biological process
    GO:0070934    CRD-mediated mRNA stabilization    An mRNA stabilization process in which one or more RNA-binding proteins associate with a sequence in the open reading frame called the coding region instability determinant (CRD).
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces 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:0097150    neuronal stem cell population maintenance    Any process in by an organism or tissue maintains a population of neuronal stem cells.
    GO:0022013    pallium cell proliferation in forebrain    The multiplication or reproduction of pallium cells in the forebrain, resulting in the expansion of the cell population.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0010610    regulation of mRNA stability involved in response to stress    Any process that modulates the propensity of mRNA molecules to degradation that is part of a change in state or activity of a cell as a result of an exogenous disturbance.
    GO:0006417    regulation of translation    Any process that modulates 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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0070937    CRD-mediated mRNA stability complex    A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, it may consist of IGF2BP1, HNRNPU, SYNCRIP/HNRNPQ, YBX1, and DHX9.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2B1_CHICK | O422542n8m

(-) Related Entries Specified in the PDB File

2n8m