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PDBsum entry 1yvp

Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
RNA binding protein/RNA PDB id
1yvp
Jmol
Contents
Protein chains
529 a.a. *
DNA/RNA
Ligands
ACT ×2
Metals
_MG ×2
Waters ×408
* Residue conservation analysis
PDB id:
1yvp
Name: RNA binding protein/RNA
Title: Ro autoantigen complexed with rnas
Structure: Y RNA sequence, first strand. Chain: c, e, g, h. Engineered: yes. Other_details: chains g and h are single strands bound by p y RNA sequence, second strand. Chain: d, f. Engineered: yes. 60-kda ss-a/ro ribonucleoprotein. Chain: a, b.
Source: Synthetic: yes. Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: tn5 b1-4. Expression_system_organ: eggs.
Biol. unit: Tetramer (from PQS)
Resolution:
2.20Å     R-factor:   0.202     R-free:   0.238
Authors: A.J.Stein,G.Fuchs,C.Fu,S.L.Wolin,K.M.Reinisch
Key ref:
A.J.Stein et al. (2005). Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity. Cell, 121, 529-539. PubMed id: 15907467 DOI: 10.1016/j.cell.2005.03.009
Date:
16-Feb-05     Release date:   07-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P42700  (RO60_XENLA) -  60 kDa SS-A/Ro ribonucleoprotein
Seq:
Struc:
 
Seq:
Struc:
538 a.a.
529 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonucleoprotein complex   2 terms 
  Biological process     cell projection organization   1 term 
  Biochemical function     RNA binding     3 terms  

 

 
DOI no: 10.1016/j.cell.2005.03.009 Cell 121:529-539 (2005)
PubMed id: 15907467  
 
 
Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity.
A.J.Stein, G.Fuchs, C.Fu, S.L.Wolin, K.M.Reinisch.
 
  ABSTRACT  
 
The Ro 60 kDa autoantigen is a major target of the immune response in patients with systemic lupus erythematosus. In vertebrate cells, Ro binds misfolded small RNAs and likely functions in RNA quality control. In eukaryotes and bacteria, Ro also associates with small RNAs called Y RNAs. We present structures of unliganded Ro and Ro complexed with two RNAs at 1.95 and 2.2 A resolution, respectively. Ro consists of a von Willebrand factor A domain and a doughnut-shaped domain composed of HEAT repeats. In the complex, a fragment of Y RNA binds on the outer surface of the HEAT-repeat ring, and single-stranded RNA binds in the toroid hole. Mutagenesis supports a binding site for misfolded RNAs that encompasses both sites, with a single-stranded end inserted into the toroid cavity. Our experiments suggest that one role of Y RNAs may be to regulate access of other RNAs to Ro.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structures of Ro and the Ro/RNA Complex
Figure 3.
Figure 3. The MIDAS Motif
 
  The above figures are reprinted by permission from Cell Press: Cell (2005, 121, 529-539) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21060685 A.R.Langley, H.Chambers, C.P.Christov, and T.Krude (2010).
Ribonucleoprotein particles containing non-coding Y RNAs, Ro60, La and nucleolin are not required for Y RNA function in DNA replication.
  PLoS One, 5, e13673.  
20160119 E.J.Wurtmann, and S.L.Wolin (2010).
A role for a bacterial ortholog of the Ro autoantigen in starvation-induced rRNA degradation.
  Proc Natl Acad Sci U S A, 107, 4022-4027.  
20349053 I.Boria, A.R.Gruber, A.Tanzer, S.H.Bernhart, R.Lorenz, M.M.Mueller, I.L.Hofacker, and P.F.Stadler (2010).
Nematode sbRNAs: homologs of vertebrate Y RNAs.
  J Mol Evol, 70, 346-358.  
20629708 J.G.Routsias, and A.G.Tzioufas (2010).
Autoimmune response and target autoantigens in Sjogren's syndrome.
  Eur J Clin Invest, 40, 1026-1036.  
20643529 J.G.Routsias, and A.G.Tzioufas (2010).
B-cell epitopes of the intracellular autoantigens Ro/SSA and La/SSB: tools to study the regulation of the autoimmune response.
  J Autoimmun, 35, 256-264.  
20031372 M.H.Hoffmann, S.Trembleau, S.Muller, and G.Steiner (2010).
Nucleic acid-associated autoantigens: pathogenic involvement and therapeutic potential.
  J Autoimmun, 34, J178-J206.  
19776129 E.L.Garcia, A.Onafuwa-Nuga, S.Sim, S.R.King, S.L.Wolin, and A.Telesnitsky (2009).
Packaging of host mY RNAs by murine leukemia virus may occur early in Y RNA biogenesis.
  J Virol, 83, 12526-12534.  
19248095 J.H.Reed, B.Giannakopoulos, M.W.Jackson, S.A.Krilis, and T.P.Gordon (2009).
Ro 60 functions as a receptor for beta(2)-glycoprotein I on apoptotic cells.
  Arthritis Rheum, 60, 860-869.  
19248093 R.M.Clancy (2009).
When the levee doesn't break: a novel role of beta2-glycoprotein I to protect against congenital heart block.
  Arthritis Rheum, 60, 636-638.  
19635865 S.Bolland, and A.Garcia-Sastre (2009).
Vicious circle: systemic autoreactivity in Ro52/TRIM21-deficient mice.
  J Exp Med, 206, 1647-1651.  
19116308 S.Sim, D.E.Weinberg, G.Fuchs, K.Choi, J.Chung, and S.L.Wolin (2009).
The subcellular distribution of an RNA quality control protein, the Ro autoantigen, is regulated by noncoding Y RNA binding.
  Mol Biol Cell, 20, 1555-1564.  
19474146 T.J.Gardiner, C.P.Christov, A.R.Langley, and T.Krude (2009).
A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication.
  RNA, 15, 1375-1385.  
18442490 G.W.Jawdekar, and R.W.Henry (2008).
Transcriptional regulation of human small nuclear RNA genes.
  Biochim Biophys Acta, 1779, 295-305.  
18950732 J.R.Hogg, and K.Collins (2008).
Structured non-coding RNAs and the RNP Renaissance.
  Curr Opin Chem Biol, 12, 684-689.  
17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
  Front Biosci, 13, 1.  
17392270 A.Ramesh, C.G.Savva, A.Holzenburg, and J.C.Sacchettini (2007).
Crystal structure of Rsr, an ortholog of the antigenic Ro protein, links conformational flexibility to RNA binding activity.
  J Biol Chem, 282, 14960-14967.
PDB code: 2nvo
17655690 C.Pichon, and B.Felden (2007).
Proteins that interact with bacterial small RNA regulators.
  FEMS Microbiol Rev, 31, 614-625.  
17960235 H.Bhaskaran, and R.Russell (2007).
Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone.
  Nature, 449, 1014-1018.  
17992591 J.G.Routsias, and A.G.Tzioufas (2007).
Sjögren's syndrome--study of autoantigens and autoantibodies.
  Clin Rev Allergy Immunol, 32, 238-251.  
18056422 J.R.Hogg, and K.Collins (2007).
Human Y5 RNA specializes a Ro ribonucleoprotein for 5S ribosomal RNA quality control.
  Genes Dev, 21, 3067-3072.  
17395456 K.M.Reinisch, and S.L.Wolin (2007).
Emerging themes in non-coding RNA quality control.
  Curr Opin Struct Biol, 17, 209-214.  
17438300 P.T.Li, C.Bustamante, and I.Tinoco (2007).
Real-time control of the energy landscape by force directs the folding of RNA molecules.
  Proc Natl Acad Sci U S A, 104, 7039-7044.  
18086320 R.Lafyatis, and A.Marshak-Rothstein (2007).
Toll-like receptors and innate immune responses in systemic lupus erythematosus.
  Arthritis Res Ther, 9, 222.  
17510283 X.Chen, E.J.Wurtmann, J.Van Batavia, B.Zybailov, M.P.Washburn, and S.L.Wolin (2007).
An ortholog of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans.
  Genes Dev, 21, 1328-1339.  
16929303 C.B.Andersen, T.Becker, M.Blau, M.Anand, M.Halic, B.Balar, T.Mielke, T.Boesen, J.S.Pedersen, C.M.Spahn, T.G.Kinzy, G.R.Andersen, and R.Beckmann (2006).
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
  Nature, 443, 663-668.
PDB codes: 2iw3 2iwh 2ix3 2ix8
16943439 C.P.Christov, T.J.Gardiner, D.Szüts, and T.Krude (2006).
Functional requirement of noncoding Y RNAs for human chromosomal DNA replication.
  Mol Cell Biol, 26, 6993-7004.  
17072315 E.Berezikov, F.Thuemmler, L.W.van Laake, I.Kondova, R.Bontrop, E.Cuppen, and R.H.Plasterk (2006).
Diversity of microRNAs in human and chimpanzee brain.
  Nat Genet, 38, 1375-1377.  
17041599 G.Fuchs, A.J.Stein, C.Fu, K.M.Reinisch, and S.L.Wolin (2006).
Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen.
  Nat Struct Mol Biol, 13, 1002-1009.
PDB code: 2i91
17381339 G.J.Hannon, F.V.Rivas, E.P.Murchison, and J.A.Steitz (2006).
The expanding universe of noncoding RNAs.
  Cold Spring Harb Symp Quant Biol, 71, 551-564.  
16477017 J.E.Gottenberg, N.Cagnard, C.Lucchesi, F.Letourneur, S.Mistou, T.Lazure, S.Jacques, N.Ba, M.Ittah, C.Lepajolec, M.Labetoulle, M.Ardizzone, J.Sibilia, C.Fournier, G.Chiocchia, and X.Mariette (2006).
Activation of IFN pathways and plasmacytoid dendritic cell recruitment in target organs of primary Sjögren's syndrome.
  Proc Natl Acad Sci U S A, 103, 2770-2775.  
16645989 K.M.Kelly, H.Zhuang, D.C.Nacionales, P.O.Scumpia, R.Lyons, J.Akaogi, P.Lee, B.Williams, M.Yamamoto, S.Akira, M.Satoh, and W.H.Reeves (2006).
"Endogenous adjuvant" activity of the RNA components of lupus autoantigens Sm/RNP and Ro 60.
  Arthritis Rheum, 54, 1557-1567.  
16923390 M.A.Schumacher, E.Karamooz, A.Zíková, L.Trantírek, and J.Lukes (2006).
Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism.
  Cell, 126, 701-711.
PDB codes: 2gia 2gid 2gje
17381333 S.L.Wolin, and E.J.Wurtmann (2006).
Molecular chaperones and quality control in noncoding RNA biogenesis.
  Cold Spring Harb Symp Quant Biol, 71, 505-511.  
16890888 S.L.Wolin, and K.M.Reinisch (2006).
The Ro 60 kDa autoantigen comes into focus: interpreting epitope mapping experiments on the basis of structure.
  Autoimmun Rev, 5, 367-372.  
17098186 T.A.Springer (2006).
Complement and the multifaceted functions of VWA and integrin I domains.
  Structure, 14, 1611-1616.  
16227273 A.A.Onafuwa-Nuga, S.R.King, and A.Telesnitsky (2005).
Nonrandom packaging of host RNAs in moloney murine leukemia virus.
  J Virol, 79, 13528-13537.  
15999107 G.J.Pruijn (2005).
Doughnuts dealing with RNA.
  Nat Struct Mol Biol, 12, 562-564.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.