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PDBsum entry 1s79

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protein links
RNA binding protein, translation PDB id
1s79
Jmol
Contents
Protein chain
103 a.a. *
* Residue conservation analysis
PDB id:
1s79
Name: RNA binding protein, translation
Title: Solution structure of the central rrm of human la protein
Structure: Lupus la protein. Chain: a. Fragment: central rrm. Synonym: sjogren syndrome type b antigen, ss-b, la ribonucleoprotein, la autoantigen. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ssb. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: C.Alfano,D.Sanfelice,J.Babon,G.Kelly,A.Jacks,S.Curry, M.R.Conte
Key ref:
C.Alfano et al. (2004). Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein. Nat Struct Mol Biol, 11, 323-329. PubMed id: 15004549 DOI: 10.1038/nsmb747
Date:
29-Jan-04     Release date:   06-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05455  (LA_HUMAN) -  Lupus La protein
Seq:
Struc:
408 a.a.
103 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

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

 

 
DOI no: 10.1038/nsmb747 Nat Struct Mol Biol 11:323-329 (2004)
PubMed id: 15004549  
 
 
Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein.
C.Alfano, D.Sanfelice, J.Babon, G.Kelly, A.Jacks, S.Curry, M.R.Conte.
 
  ABSTRACT  
 
The La protein is a conserved component of eukaryotic ribonucleoprotein complexes that binds the 3' poly(U)-rich elements of nascent RNA polymerase III (pol III) transcripts to assist folding and maturation. This specific recognition is mediated by the N-terminal domain (NTD) of La, which comprises a La motif and an RNA recognition motif (RRM). We have determined the solution structures of both domains and show that the La motif adopts an alpha/beta fold that comprises a winged-helix motif elaborated by the insertion of three helices. Chemical shift mapping experiments show that these insertions are involved in RNA interactions. They further delineate a distinct surface patch on each domain-containing both basic and aromatic residues-that interacts with RNA and accounts for the cooperative binding of short oligonucleotides exhibited by the La NTD.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Domain organization of human La and deletion mutants used in this study. Conventionally1, 2 human La is divided in two halves, N-terminal domain, comprising the La motif (domain 1) and the adjacent RRM (domain 2), and C-terminal domain, encompassing the RRM (domain 3), the SBM and the NLS (see text).
Figure 4.
Figure 4. Alignment of the La motif and central RRM sequences for La homologs.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 323-329) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21212361 N.J.Kucera, M.E.Hodsdon, and S.L.Wolin (2011).
An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors.
  Proc Natl Acad Sci U S A, 108, 1308-1313.  
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.  
20573744 K.Schäffler, K.Schulz, A.Hirmer, J.Wiesner, M.Grimm, A.Sickmann, and U.Fischer (2010).
A stimulatory role for the La-related protein 4B in translation.
  RNA, 16, 1488-1499.  
20168331 Y.He, G.R.Andersen, and K.H.Nielsen (2010).
Structural basis for the function of DEAH helicases.
  EMBO Rep, 11, 180-186.
PDB code: 3kx2
19299548 C.Bousquet-Antonelli, and J.M.Deragon (2009).
A comprehensive analysis of the La-motif protein superfamily.
  RNA, 15, 750-764.  
18836485 F.Brenet, N.D.Socci, N.Sonenberg, and E.C.Holland (2009).
Akt phosphorylation of La regulates specific mRNA translation in glial progenitors.
  Oncogene, 28, 128-139.  
19096764 H.Weng, C.Kim, C.Valavanis, Z.Wang, and L.M.Schwartz (2009).
Acheron, an novel LA antigen family member, binds to CASK and forms a complex with Id transcription factors.
  Cell Mol Biol Lett, 14, 273-287.  
19287396 M.A.Bayfield, and R.J.Maraia (2009).
Precursor-product discrimination by La protein during tRNA metabolism.
  Nat Struct Mol Biol, 16, 430-437.  
18515547 K.Nykamp, M.H.Lee, and J.Kimble (2008).
C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis.
  RNA, 14, 1378-1389.  
18547518 O.Kotik-Kogan, E.R.Valentine, D.Sanfelice, M.R.Conte, and S.Curry (2008).
Structural analysis reveals conformational plasticity in the recognition of RNA 3' ends by the human La protein.
  Structure, 16, 852-862.
PDB codes: 2vod 2von 2voo 2vop
18829760 T.Mondal, U.Ray, A.K.Manna, R.Gupta, S.Roy, and S.Das (2008).
Structural determinant of human La protein critical for internal initiation of translation of hepatitis C virus RNA.
  J Virol, 82, 11927-11938.  
17992591 J.G.Routsias, and A.G.Tzioufas (2007).
Sjögren's syndrome--study of autoantigens and autoantibodies.
  Clin Rev Allergy Immunol, 32, 238-251.  
17951964 K.Ichihara, H.Shimizu, O.Taguchi, M.Yamaguchi, and Y.H.Inoue (2007).
A Drosophila orthologue of larp protein family is required for multiple processes in male meiosis.
  Cell Struct Funct, 32, 89.  
17308035 M.A.Bayfield, T.E.Kaiser, R.V.Intine, and R.J.Maraia (2007).
Conservation of a masked nuclear export activity of La proteins and its effects on tRNA maturation.
  Mol Cell Biol, 27, 3303-3312.  
17459889 S.Fleurdépine, J.M.Deragon, M.Devic, J.Guilleminot, and C.Bousquet-Antonelli (2007).
A bona fide La protein is required for embryogenesis in Arabidopsis thaliana.
  Nucleic Acids Res, 35, 3306-3321.  
17059594 C.R.Bradshaw, V.Surendranath, and B.Habermann (2006).
ProFAT: a web-based tool for the functional annotation of protein sequences.
  BMC Bioinformatics, 7, 466.  
16449655 J.M.Park, M.J.Kohn, M.W.Bruinsma, C.Vech, R.V.Intine, S.Fuhrmann, A.Grinberg, I.Mukherjee, P.E.Love, M.S.Ko, M.L.DePamphilis, and R.J.Maraia (2006).
The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells.
  Mol Cell Biol, 26, 1445-1451.  
16387655 M.Teplova, Y.R.Yuan, A.T.Phan, L.Malinina, S.Ilin, A.Teplov, and D.J.Patel (2006).
Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.
  Mol Cell, 21, 75-85.
PDB codes: 1yty 1zh5
16427005 R.J.Maraia, and M.A.Bayfield (2006).
The La protein-RNA complex surfaces.
  Mol Cell, 21, 149-152.  
16679019 S.Curry, and M.R.Conte (2006).
A terminal affair: 3'-end recognition by the human La protein.
  Trends Biochem Sci, 31, 303-305.  
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.  
16799560 Y.Huang, M.A.Bayfield, R.V.Intine, and R.J.Maraia (2006).
Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation.
  Nat Struct Mol Biol, 13, 611-618.  
16107699 F.Brenet, N.Dussault, J.Borch, G.Ferracci, C.Delfino, P.Roepstorff, R.Miquelis, and L.Ouafik (2005).
Mammalian peptidylglycine alpha-amidating monooxygenase mRNA expression can be modulated by the La autoantigen.
  Mol Cell Biol, 25, 7505-7521.  
16281058 J.Deng, N.L.Ernst, S.Turley, K.D.Stuart, and W.G.Hol (2005).
Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei.
  EMBO J, 24, 4007-4017.
PDB codes: 2b4v 2b51 2b56
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
16294247 M.Hedenström, H.Emtenäs, N.Pemberton, V.Aberg, S.J.Hultgren, J.S.Pinkner, V.Tegman, F.Almqvist, I.Sethson, and J.Kihlberg (2005).
NMR studies of interactions between periplasmic chaperones from uropathogenic E. coli and pilicides that interfere with chaperone function and pilus assembly.
  Org Biomol Chem, 3, 4193-4200.  
15665870 S.Yoshizawa, L.Rasubala, T.Ose, D.Kohda, D.Fourmy, and K.Maenaka (2005).
Structural basis for mRNA recognition by elongation factor SelB.
  Nat Struct Mol Biol, 12, 198-203.
PDB code: 1wsu
15572691 R.V.Intine, M.Dundr, A.Vassilev, E.Schwartz, Y.Zhao, Y.Zhao, M.L.Depamphilis, and R.J.Maraia (2004).
Nonphosphorylated human La antigen interacts with nucleolin at nucleolar sites involved in rRNA biogenesis.
  Mol Cell Biol, 24, 10894-10904.  
15450741 V.R.Iyer (2004).
Exploring the post-transcriptional RNA world with DNA microarrays.
  Trends Biotechnol, 22, 498-500.  
15299008 Y.Iko, T.S.Kodama, N.Kasai, T.Oyama, E.H.Morita, T.Muto, M.Okumura, R.Fujii, T.Takumi, S.Tate, and K.Morikawa (2004).
Domain architectures and characterization of an RNA-binding protein, TLS.
  J Biol Chem, 279, 44834-44840.  
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.