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PDBsum entry 1sxl

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protein links
RNA-binding protein PDB id
1sxl
Jmol
Contents
Protein chain
97 a.a. *
* Residue conservation analysis
PDB id:
1sxl
Name: RNA-binding protein
Title: Resonance assignments and solution structure of the second RNA-binding domain of sex-lethal determined by multidimensional heteronuclear magnetic resonance spectroscopy
Structure: Sex-lethal protein protein. Chain: a. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: sex-lethal
NMR struc: 17 models
Authors: A.L.Lee,R.Kanaar,D.C.Rio,D.E.Wemmer
Key ref:
A.L.Lee et al. (1994). Resonance assignments and solution structure of the second RNA-binding domain of sex-lethal determined by multidimensional heteronuclear magnetic resonance. Biochemistry, 33, 13775-13786. PubMed id: 7524663 DOI: 10.1021/bi00250a031
Date:
01-Jul-94     Release date:   30-Sep-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19339  (SXL_DROME) -  Protein sex-lethal
Seq:
Struc:
354 a.a.
97 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1021/bi00250a031 Biochemistry 33:13775-13786 (1994)
PubMed id: 7524663  
 
 
Resonance assignments and solution structure of the second RNA-binding domain of sex-lethal determined by multidimensional heteronuclear magnetic resonance.
A.L.Lee, R.Kanaar, D.C.Rio, D.E.Wemmer.
 
  ABSTRACT  
 
The RNA-binding protein Sex-lethal (Sxl) is a critical regulator of sexual differentiation and dosage compensation in Drosophila. This regulatory activity is a consequence of the ability of Sxl to bind uridine-rich RNA tracts involved in pre-mRNA splicing. Sxl contains two RNP consensus-type RNA-binding domains (RBDs). A structural study of a portion of Sxl (amino acids 199-294) containing the second RNA-binding domain (RBD-2) using multidimensional heteronuclear NMR is presented here. Nearly complete 1H, 13C, and 15N resonance assignments have been obtained from 15N- and 13C/15N-uniformly labeled protein. These assignments were used to analyze 3D 15N-separated NOESY and 13C/13C-separated 4D NOESY spectra which produced 494 total and 169 long-range NOE-derived distance restraints. Along with 41 backbone dihedral restraints, these distance restraints were employed to generate an intermediate-resolution family of calculated structures, which exhibits the beta alpha beta-beta alpha beta tertiary fold found in other RBD-containing proteins. The RMSD to the average structure for the backbone atoms of residues 11-93 is 1.55 +/- 0.30 A, while the RMSD for backbone atoms involved in secondary structure is 0.76 +/- 0.14 A. A capping box [Harper, E.T., & Rose, G.D. (1993) Biochemistry 32, 7605-7609] was identified at the N-terminus of the first helix and has been characterized by short- and medium-range NOEs. Finally, significant structural similarities and differences between Sxl RBD-2 and other RBD-containing proteins are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16362043 F.Vitali, A.Henning, F.C.Oberstrass, Y.Hargous, S.D.Auweter, M.Erat, and F.H.Allain (2006).
Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling.
  EMBO J, 25, 150-162.
PDB code: 2evz
12704645 A.Bevilacqua, M.C.Ceriani, S.Capaccioli, and A.Nicolin (2003).
Post-transcriptional regulation of gene expression by degradation of messenger RNAs.
  J Cell Physiol, 195, 356-372.  
12809490 G.C.Pérez-Alvarado, M.Martínez-Yamout, M.M.Allen, R.Grosschedl, H.J.Dyson, and P.E.Wright (2003).
Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.
  Biochemistry, 42, 7348-7357.
PDB code: 1no8
12554879 H.Banerjee, A.Rahn, W.Davis, and R.Singh (2003).
Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding.
  RNA, 9, 88-99.  
11917013 J.Vitali, J.Ding, J.Jiang, Y.Zhang, A.R.Krainer, and R.M.Xu (2002).
Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.
  Nucleic Acids Res, 30, 1531-1538.
PDB code: 1l3k
10734193 M.Inoue, Y.Muto, H.Sakamoto, and S.Yokoyama (2000).
NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C.
  Nucleic Acids Res, 28, 1743-1750.
PDB codes: 1d8z 1d9a
10588732 E.Welin Henriksson, M.Wahren-Herlenius, I.Lundberg, E.Mellquist, and I.Pettersson (1999).
Key residues revealed in a major conformational epitope of the U1-70K protein.
  Proc Natl Acad Sci U S A, 96, 14487-14492.  
10585411 N.J.Richter, G.W.Rogers, J.O.Hensold, and W.C.Merrick (1999).
Further biochemical and kinetic characterization of human eukaryotic initiation factor 4H.
  J Biol Chem, 274, 35415-35424.  
10220389 S.M.Crowder, R.Kanaar, D.C.Rio, and T.Alber (1999).
Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal.
  Proc Natl Acad Sci U S A, 96, 4892-4897.
PDB code: 3sxl
10102992 S.W.Chi, Y.Muto, M.Inoue, I.Kim, H.Sakamoto, Y.Shimura, S.Yokoyama, B.S.Choi, and H.Kim (1999).
Chemical shift perturbation studies of the interactions of the second RNA-binding domain of the Drosophila sex-lethal protein with the transformer pre-mRNA polyuridine tract and 3' splice-site sequences.
  Eur J Biochem, 260, 649-660.  
10449418 T.Ito, Y.Muto, M.R.Green, and S.Yokoyama (1999).
Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).
  EMBO J, 18, 4523-4534.
PDB codes: 1u2f 2u2f
9587002 D.M.Briercheck, T.C.Wood, T.J.Allison, J.P.Richardson, and G.S.Rule (1998).
The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions.
  Nat Struct Biol, 5, 393-399.
PDB code: 1a63
9646873 G.Varani, and K.Nagai (1998).
RNA recognition by RNP proteins during RNA processing.
  Annu Rev Biophys Biomol Struct, 27, 407-445.  
9592147 M.Samuels, G.Deshpande, and P.Schedl (1998).
Activities of the Sex-lethal protein in RNA binding and protein:protein interactions.
  Nucleic Acids Res, 26, 2625-2637.  
9312154 C.Sun, and J.L.Woolford (1997).
The yeast nucleolar protein Nop4p contains four RNA recognition motifs necessary for ribosome biogenesis.
  J Biol Chem, 272, 25345-25352.  
9148924 G.Serin, G.Joseph, L.Ghisolfi, M.Bauzan, M.Erard, F.Amalric, and P.Bouvet (1997).
Two RNA-binding domains determine the RNA-binding specificity of nucleolin.
  J Biol Chem, 272, 13109-13116.  
9305981 I.Pérez, J.G.McAfee, and J.G.Patton (1997).
Multiple RRMs contribute to RNA binding specificity and affinity for polypyrimidine tract binding protein.
  Biochemistry, 36, 11881-11890.  
9265619 J.Lu, and K.B.Hall (1997).
Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy.
  Biochemistry, 36, 10393-10405.
PDB code: 2u1a
9127942 J.Lu, and K.B.Hall (1997).
Thermal unfolding of the N-terminal RNA binding domain of the human U1A protein studied by differential scanning calorimetry.
  Biophys Chem, 64, 111-119.  
9311984 P.Bouvet, C.Jain, J.G.Belasco, F.Amalric, and M.Erard (1997).
RNA recognition by the joint action of two nucleolin RNA-binding domains: genetic analysis and structural modeling.
  EMBO J, 16, 5235-5246.  
  9426195 P.Oberosler, and W.Nellen (1997).
Functional activity and developmental regulation of DdRBP1, a RNA binding protein in Dictyostelium discoideum.
  Biol Chem, 378, 1353-1360.  
9115444 R.M.Xu, L.Jokhan, X.Cheng, A.Mayeda, and A.R.Krainer (1997).
Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs.
  Structure, 5, 559-570.
PDB code: 1up1
9164463 Y.Shamoo, U.Krueger, L.M.Rice, K.R.Williams, and T.A.Steitz (1997).
Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 A resolution.
  Nat Struct Biol, 4, 215-222.
PDB code: 1ha1
  8844847 J.K.Kranz, J.Lu, and K.B.Hall (1996).
Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain.
  Protein Sci, 5, 1567-1583.  
8696973 K.Nagai (1996).
RNA-protein complexes.
  Curr Opin Struct Biol, 6, 53-61.  
7543225 K.Nagai, C.Oubridge, N.Ito, J.Avis, and P.Evans (1995).
The RNP domain: a sequence-specific RNA-binding domain involved in processing and transport of RNA.
  Trends Biochem Sci, 20, 235-240.  
  8582616 M.L.Samson, M.J.Lisbin, and K.White (1995).
Two distinct temperature-sensitive alleles at the elav locus of Drosophila are suppressed nonsense mutations of the same tryptophan codon.
  Genetics, 141, 1101-1111.  
  7556096 R.Kanaar, A.L.Lee, D.Z.Rudner, D.E.Wemmer, and D.C.Rio (1995).
Interaction of the sex-lethal RNA binding domains with RNA.
  EMBO J, 14, 4530-4539.  
8535784 T.Gallagher, G.Gilliland, L.Wang, and P.Bryan (1995).
The prosegment-subtilisin BPN' complex: crystal structure of a specific 'foldase'.
  Structure, 3, 907-914.
PDB code: 1spb
  7565780 X.Peng, and S.M.Mount (1995).
Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor.
  Mol Cell Biol, 15, 6273-6282.  
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.