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(-) Description

Title :  RO AUTOANTIGEN
 
Authors :  A. J. Stein, G. Fuchs, C. Fu, S. L. Wolin, K. M. Reinisch
Date :  16 Feb 05  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Heat Repeat; Von Willebrand Factor A; Rossmann Fold; Midas Motif', Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, G. Fuchs, C. Fu, S. L. Wolin, K. M. Reinisch
Structural Insights Into Rna Quality Control: The Ro Autoantigen Binds Misfolded Rnas Via Its Central Cavity
Cell(Cambridge, Mass. ) V. 121 529 2005
PubMed-ID: 15907467  |  Reference-DOI: 10.1016/J.CELL.2005.03.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 60-KDA SS-A/RO RIBONUCLEOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Other Details: PROTEIN A BINDS RNA CHAIN G, B BINDS H
    Synonym: RO AUTOANTIGEN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YVR)

(-) Sites  (0, 0)

(no "Site" information available for 1YVR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YVR)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TROVEPS50988 TROVE domain profile.RO60_XENLA16-369  1A:16-369

(-) Exons   (0, 0)

(no "Exon" information available for 1YVR)

(-) 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:520
 aligned with RO60_XENLA | P42700 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:533
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   
           RO60_XENLA     5 MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGNRGKLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
               SCOP domains d1yvra1 A:5-363 60-kda SS-aARo ribonucleoprotein                                                                                                                                                                                                                                                                                                                       d1yvra2 A:364-537 60-kda SS-A/Ro ribonucleoprotein, RoRNP                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------TROVE-1yvrA01 A:16-369                                                                                                                                                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........ee.....eeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh--------.hhhhhhhhhhhhhh.hhhhhhhhhh........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.-----.....hhhhhhhhhhhhhhh..........eeeeee.hhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee...ee........hhhhhhhhhh.........hhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhh...eeeeee.....ee........eeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------TROVE  PDB: A:16-369 UniProt: 16-369                                                                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yvr A   5 MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDL--------WGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGH-----LRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDL 537
                                    14        24        34        44        54        64        74        84        94       104       114       124       134|      144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334|     |344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534   
                                                                                                                                                            135      144                                                                                                                                                                                            335   341
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YVR)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: TROVE] (3)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RO60_XENLA | P42700)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0034336    misfolded RNA binding    Interacting selectively and non-covalently with an RNA molecule that has assumed an incorrect conformation.
biological process
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.

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  1yvr
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 Related Entries

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

UniProtKB/Swiss-Prot
        RO60_XENLA | P42700: 1yvp 2i91

(-) Related Entries Specified in the PDB File

1yvp RO AUTOANTIGEN COMPLEXED WITH RNAS