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(-) Description

Title :  THE PABC1 MLLE DOMAIN BOUND TO THE VARIANT PAM2 MOTIF OF LARP4B
 
Authors :  C. Grimm, J. P. Pelz
Date :  03 Dec 10  (Deposition) - 21 Dec 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mlle Domain, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Grimm, J. P. Pelz
Larp4B Binds To The Pabc1 Mlle Domain Via A Variant Pam2 Motif
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLYADENYLATE-BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentUNP RESIDUES 543-621
    GenePABPC1, PAB1, PABP1, PABPC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPABP-1, POLY(A)-BINDING PROTEIN 1
 
Molecule 2 - LA-RELATED PROTEIN 4B
    ChainsB
    EngineeredYES
    FragmentUNP RESIDUES 55-69
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLA RIBONUCLEOPROTEIN DOMAIN FAMILY MEMBER 4B, LA RIBONUCLEOPROTEIN DOMAIN FAMILY MEMBER 5, LA-RELATED PROTEIN 5
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3PTH)

(-) Sites  (0, 0)

(no "Site" information available for 3PTH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1eENST000003186071eENSE00002107718chr8:101734940-1017336191322PABP1_HUMAN1-65650--
1.2eENST000003186072eENSE00002179154chr8:101730508-101730315194PABP1_HUMAN65-129650--
1.2iENST000003186072iENSE00001088711chr8:101730116-101730001116PABP1_HUMAN130-168390--
1.3bENST000003186073bENSE00001676241chr8:101727829-101727690140PABP1_HUMAN168-215480--
1.4cENST000003186074cENSE00001088702chr8:101725409-10172531595PABP1_HUMAN215-246320--
1.5aENST000003186075aENSE00001088717chr8:101725017-101724880138PABP1_HUMAN247-292460--
1.6aENST000003186076aENSE00001088710chr8:101724685-10172459096PABP1_HUMAN293-324320--
1.7bENST000003186077bENSE00002184139chr8:101721959-101721687273PABP1_HUMAN325-415910--
1.8cENST000003186078cENSE00001088708chr8:101721451-10172136191PABP1_HUMAN416-446310--
1.9bENST000003186079bENSE00001088705chr8:101719225-101719115111PABP1_HUMAN446-483380--
1.10bENST0000031860710bENSE00002199412chr8:101719033-101718879155PABP1_HUMAN483-534520--
1.11ENST0000031860711ENSE00001088703chr8:101717901-10171781785PABP1_HUMAN535-563291A:544-56320
1.12aENST0000031860712aENSE00001088713chr8:101717284-101717154131PABP1_HUMAN563-606441A:563-60644
1.13aENST0000031860713aENSE00001088716chr8:101716618-10171652594PABP1_HUMAN607-636301A:607-61812
1.14eENST0000031860714eENSE00001378950chr8:101715587-101715144444PABP1_HUMAN-00--

(-) 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:75
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:75
                                   553       563       573       583       593       603       613     
          PABP1_HUMAN   544 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQ 618
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11           -------------------------------------------Exon 1.13a   Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.12a  PDB: A:563-606 UniProt: 563-606 ------------ Transcript 1 (2)
                 3pth A 544 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQ 618
                                   553       563       573       583       593       603       613     

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with LAR4B_HUMAN | Q92615 from UniProtKB/Swiss-Prot  Length:738

    Alignment length:15
                                    64     
          LAR4B_HUMAN    55 ELNPNAEVWGAPVLH  69
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 3pth B  55 ELNPNAEVWGAPVLH  69
                                    64     

   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 3PTH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PABP1_HUMAN | P11940)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0008143    poly(A) binding    Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
    GO:0008266    poly(U) RNA binding    Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0008494    translation activator activity    Any of a group of soluble proteins functioning in the activation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0048255    mRNA stabilization    Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
    GO:2000623    negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    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:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
    GO:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0036464    cytoplasmic ribonucleoprotein granule    A ribonucleoprotein granule located in the cytoplasm.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

Chain B   (LAR4B_HUMAN | Q92615)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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).
biological process
    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: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.
cellular component
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0042788    polysomal ribosome    A ribosome bound to mRNA that forms part of a polysome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PABP1_HUMAN | P119401cvj 1g9l 1jgn 1jh4 2k8g 2rqg 2rqh 2x04 3ktp 3ktr 3kui 3kuj 3kur 3kus 3kut 3pkn 4f02 4f25 4f26 5dx1 5dx8 5dxa 5lgp 5lgq 5lgr 5lgs

(-) Related Entries Specified in the PDB File

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