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(-) Description

Title :  NMR STRUCTURE OF THE LA MOTIF OF HUMAN LA PROTEIN
 
Authors :  C. Alfano, D. Sanfelice, J. Babon, G. Kelly, A. Jacks, S. Curry, M. R. Conte
Date :  29 Jan 04  (Deposition) - 06 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  La Motif, Alpha/Beta, Winged Helix Domain, Rna Binding Protein, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Alfano, D. Sanfelice, J. Babon, G. Kelly, A. Jacks, S. Curry, M. R. Conte
Structural Analysis Of Cooperative Rna Binding By The La Motif And Central Rrm Domain Of Human La Protein.
Nat. Struct. Mol. Biol. V. 11 323 2004
PubMed-ID: 15004549  |  Reference-DOI: 10.1038/NSMB747
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LUPUS LA PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector: PET30
    Fragment: LA MOTIF
    Gene: SSB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SJOGREN SYNDROME TYPE B ANTIGEN, SS-B, LA RIBONUCLEOPROTEIN, LA AUTOANTIGEN

 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 1S7A)

(-) Sites  (0, 0)

(no "Site" information available for 1S7A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034066P48SLA_HUMANPolymorphism17160793AP48S
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LAPS50961 La-type HTH domain profile.LA_HUMAN7-99  1A:7-99

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002609562aENSE00001893329chr2:170655322-170655486165LA_HUMAN-00--
1.4ENST000002609564ENSE00002156069chr2:170657462-17065753675LA_HUMAN1-22221A:1-2222
1.5ENST000002609565ENSE00001610086chr2:170661984-170662087104LA_HUMAN23-57351A:23-5735
1.6aENST000002609566aENSE00000782038chr2:170662175-170662349175LA_HUMAN57-115591A:57-10347
1.7cENST000002609567cENSE00000782039chr2:170663295-170663402108LA_HUMAN116-151360--
1.7gENST000002609567gENSE00002168098chr2:170663481-170663581101LA_HUMAN152-185340--
1.8cENST000002609568cENSE00000782041chr2:170664992-17066506372LA_HUMAN185-209250--
1.8eENST000002609568eENSE00000782042chr2:170665370-17066541243LA_HUMAN209-223150--
1.9cENST000002609569cENSE00000782043chr2:170666793-170666933141LA_HUMAN224-270470--
1.10bENST0000026095610bENSE00000782044chr2:170667368-170667554187LA_HUMAN271-333630--
1.11ENST0000026095611ENSE00000782045chr2:170667693-170667833141LA_HUMAN333-380480--
1.12bENST0000026095612bENSE00001588653chr2:170668178-170668574397LA_HUMAN380-408290--

(-) 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:103
 aligned with LA_HUMAN | P05455 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:103
                                    10        20        30        40        50        60        70        80        90       100   
             LA_HUMAN     1 MAENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDE 103
               SCOP domains d1s7aa_ A: Lupus La autoantigen N-terminal domain                                                       SCOP domains
               CATH domains 1s7aA00 A:1-103 'winged helix' repressor DNA binding domain                                             CATH domains
               Pfam domains ----------------La-1s7aA01 A:17-75                                         ---------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eehhhhhhhhhhhh...hhhhhhhhhhhh.....ee.....eee............. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------S------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HTH_LA  PDB: A:7-99 UniProt: 7-99                                                            ---- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:1-22 Exon 1.5  PDB: A:23-57             ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.6a  PDB: A:57-103 UniProt: 57-115        Transcript 1 (2)
                 1s7a A   1 MAENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDE 103
                                    10        20        30        40        50        60        70        80        90       100
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: La] (7)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (LA_HUMAN | P05455)
molecular function
    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: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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0075522    IRES-dependent viral translational initiation    Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0008334    histone mRNA metabolic process    The chemical reactions and pathways involving an mRNA encoding a histone.
    GO:1903608    protein localization to cytoplasmic stress granule    A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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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  1s7a
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 Related Entries

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

UniProtKB/Swiss-Prot
        LA_HUMAN | P05455: 1owx 1s79 1yty 1zh5 2vod 2von 2voo 2vop

(-) Related Entries Specified in the PDB File

6044 NMR ASSIGNMENT OF THE SAME DOMAIN
1owx STRUCTURE OF THE C-TERMINAL RRM OF THE LA PROTEIN
1s79 STRUCTURE OF THE ADJACENT RRM