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(-) Description

Title :  SOLUTION STRUCTURE OF RNA BINDING DOMAIN IN CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3
 
Authors :  K. Tsuda, T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 06  (Deposition) - 26 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rrm Domain, Rbd, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Tsuda, T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Rna Binding Domain In Cytoplasmic Polyadenylation Element Binding Protein 3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050719-10
    Expression System Vector TypePLASMID
    FragmentRNA RECOGNITION MOTIF
    GeneCPEB3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DNL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.CPEB3_HUMAN441-528
549-627
  2A:427-514
A:532-532

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002659971ENSE00001374446chr10:94050844-94050683162CPEB3_HUMAN-00--
1.3ENST000002659973ENSE00001162658chr10:94000118-939991031016CPEB3_HUMAN1-3353350--
1.4bENST000002659974bENSE00001252544chr10:93952393-93952234160CPEB3_HUMAN336-389540--
1.5ENST000002659975ENSE00000713779chr10:93940776-9394072057CPEB3_HUMAN389-408200--
1.6bENST000002659976bENSE00000713776chr10:93904842-93904702141CPEB3_HUMAN408-455481A:419-441 (gaps)43
1.7ENST000002659977ENSE00001726378chr10:93902875-9390278690CPEB3_HUMAN455-485311A:441-47131
1.8ENST000002659978ENSE00000713769chr10:93870951-93870833119CPEB3_HUMAN485-524401A:471-51040
1.9ENST000002659979ENSE00001759420chr10:93851701-93851587115CPEB3_HUMAN525-563391A:511-532 (gaps)30
1.10ENST0000026599710ENSE00000810688chr10:93841258-93841077182CPEB3_HUMAN563-623610--
1.11aENST0000026599711aENSE00001935038chr10:93812196-938093882809CPEB3_HUMAN624-698750--

(-) 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:114
 aligned with CPEB3_HUMAN | Q8NE35 from UniProtKB/Swiss-Prot  Length:698

    Alignment length:142
                                   422       432       442       452       462       472       482       492       502       512       522       532       542       552  
          CPEB3_HUMAN   413 DSHGDQALSSGLSSPTRCQNGERVERYSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDGSQPLDPRKTIFVG 554
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----...----------------...eeee......hhhhhhhhh.......ee...............eeee...hhhhhhhhhhhheee..eeeeee.......eeeeee............-.....-------. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------RRM  PDB: A:427-514 UniProt: 441-528                                                    --------------------RRM    PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:419-441 (gaps)           -----------------------------Exon 1.8  PDB: A:471-510                Exon 1.9  PDB: A:511-532 (gaps Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.7  PDB: A:441-471       --------------------------------------------------------------------- Transcript 1 (2)
                 2dnl A 419 GSSG----SSG----------------SRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMD-SGPSS-------G 532
                               |   424|        -       428       438       448       458       468       478       488       498       508       518       527   |     - |
                             422  423 |              426                                                                                                 526 | 531     532
                                    425                                                                                                                    527            

   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 2DNL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

NMR Structure(hide GO term definitions)
Chain A   (CPEB3_HUMAN | Q8NE35)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0035613    RNA stem-loop binding    Interacting selectively and non-covalently with a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
    GO:0035925    mRNA 3'-UTR AU-rich region binding    Interacting selectively and non-covalently with a region containing frequent adenine and uridine bases within the 3' untranslated region of a mRNA molecule.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    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: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:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0008135    translation factor activity, RNA binding    Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome.
    GO:0000900    translation repressor activity, nucleic acid binding    Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
biological process
    GO:0061158    3'-UTR-mediated mRNA destabilization    An mRNA destabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA.
    GO:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    GO:2000766    negative regulation of cytoplasmic translation    Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translation.
    GO:1900248    negative regulation of cytoplasmic translational elongation    Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational elongation.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0060999    positive regulation of dendritic spine development    Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:1900365    positive regulation of mRNA polyadenylation    Any process that activates or increases the frequency, rate or extent of mRNA polyadenylation.
    GO:1900153    positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
    GO:0060213    positive regulation of nuclear-transcribed mRNA poly(A) tail shortening    Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
    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:0060998    regulation of dendritic spine development    Any process that modulates the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:0048167    regulation of synaptic plasticity    A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0030014    CCR4-NOT complex    The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
    GO:0097440    apical dendrite    A dendrite that emerges near the apical pole of a neuron. In bipolar neurons, apical dendrites are located on the opposite side of the soma from the axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:1990124    messenger ribonucleoprotein complex    A ribonucleoprotein complex containing both protein and messenger RNA (mRNA) molecules.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

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        CPEB3_HUMAN | Q8NE352rug

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