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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER AUUUU
 
Authors :  O. Kotik-Kogan, E. R. Valentine, D. Sanfelice, M. R. Conte, S. Curry
Date :  19 Feb 08  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna-Binding Protein, Rna Recognition Motif, Systemic Lupus Erythematosus, Phosphoprotein, Rna Maturation, Rna Binding Protein, Nucleus, La Motif, Rna-Binding, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Kotik-Kogan, E. R. Valentine, D. Sanfelice, M. R. Conte, S. Curry
Structural Analysis Reveals Conformational Plasticity In The Recognition Of Rna 3' Ends By The Human La Protein.
Structure V. 16 852 2008
PubMed-ID: 18547518  |  Reference-DOI: 10.1016/J.STR.2008.02.021

(-) Compounds

Molecule 1 - LUPUS LA PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: N-TERMINAL DOMAIN, RESIDUES 4-194
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HUMAN LA PROTEIN, SJOEGREN SYNDROME TYPE B ANTIGEN, SS-B, LA RIBONUCLEOPROTEIN, LA AUTOANTIGEN
 
Molecule 2 - 5'-R(*AP*UP*UP*UP*UP)-3'
    Chains: B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:16 , HIS A:19BINDING SITE FOR RESIDUE SO4 A1192
2AC2SOFTWARETYR A:114 , ARG A:143 , LYS A:151 , SER A:153 , TYR A:188BINDING SITE FOR RESIDUE SO4 A1193

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.LA_HUMAN111-187  1A:111-187

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002609562aENSE00001893329chr2:170655322-170655486165LA_HUMAN-00--
1.4ENST000002609564ENSE00002156069chr2:170657462-17065753675LA_HUMAN1-22221A:8-2215
1.5ENST000002609565ENSE00001610086chr2:170661984-170662087104LA_HUMAN23-57351A:23-5735
1.6aENST000002609566aENSE00000782038chr2:170662175-170662349175LA_HUMAN57-115591A:57-11559
1.7cENST000002609567cENSE00000782039chr2:170663295-170663402108LA_HUMAN116-151361A:116-15136
1.7gENST000002609567gENSE00002168098chr2:170663481-170663581101LA_HUMAN152-185341A:152-18534
1.8cENST000002609568cENSE00000782041chr2:170664992-17066506372LA_HUMAN185-209251A:185-1917
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

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:184
 aligned with LA_HUMAN | P05455 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:184
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
             LA_HUMAN     8 EKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYFAK 191
               SCOP domains d2vopa1 A:8-103 Lupus La autoantigen N-terminal domain                                          -d2vopa2 A:105-191 Lupus LA protein                                                      SCOP domains
               CATH domains 2vopA01 A:8-90 'winged helix' repressor DNA binding domain                         ---------2vopA02 A:100-191  [code=3.30.70.330, no name defined]                                       CATH domains
               Pfam domains ---------La-2vopA02 A:17-75                                         -------------------------------------RRM_1-2vopA01 A:113-181                                              ---------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....eehhhhh.hhhhhhhh.hhhhhhhhhhh.....eee.....eeee.........hhhhhhhhhh.eeeee......hhhhhhhhhh....eeeeeeee.....eeeeeeeee.hhhhhhhhhh...........eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------S----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------RRM  PDB: A:111-187 UniProt: 111-187                                         ---- PROSITE
           Transcript 1 (1) Exon 1.4       Exon 1.5  PDB: A:23-57             ----------------------------------------------------------Exon 1.7c  PDB: A:116-151           Exon 1.7g  PDB: A:152-185         ------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6a  PDB: A:57-115 UniProt: 57-115                   ---------------------------------------------------------------------1.8c    Transcript 1 (2)
                 2vop A   8 EKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYFAK 191
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    


Chain B from PDB  Type:RNA  Length:5
                                     
                 2vop B  -5 AUUUU  -1
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: RRM (206)
(-)
Clan: no clan defined [family: La] (7)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(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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  2vop
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 Related Entries

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

UniProtKB/Swiss-Prot
        LA_HUMAN | P05455: 1owx 1s79 1s7a 1yty 1zh5 2vod 2von 2voo

(-) Related Entries Specified in the PDB File

1owx SOLUTION STRUCTURE OF THE C-TERMINAL RRM OF HUMAN LA (LA225-334)
1s79 SOLUTION STRUCTURE OF THE CENTRAL RRM OF HUMAN LA PROTEIN
1s7a NMR STRUCTURE OF THE LA MOTIF OF HUMAN LA PROTEIN
1yty STRUCTURAL BASIS FOR RECOGNITION OF UUUOH 3 '-TERMINII OFNASCENT RNA POL III TRANSCRIPTS BY LA AUTOANTIGEN
1zh5 STRUCTURAL BASIS FOR RECOGNITION OF UUUOH 3 '-TERMINII OFNASCENT RNA POL III TRANSCRIPTS BY LA AUTOANTIGEN
2vod CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER AUAUUUU
2von CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER AUAUUUU
2voo CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN COMPLEXED WITH RNA OLIGOMER UUUUUUUU