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protein dna_rna links
Cell cycle/RNA PDB id
1ekz
Jmol
Contents
Protein chain
76 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1ekz
Name: Cell cycle/RNA
Title: Nmr structure of the complex between the third dsrbd from drosophila staufen and a RNA hairpin
Structure: Maternal effect protein (staufen). Chain: a. Synonym: dsrbdiii. Engineered: yes. Staufen double-stranded RNA binding domain. Chain: b. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
NMR struc: 36 models
Authors: A.Ramos,S.Grunert,M.Bycroft,D.St Johnston,G.Varani
Key ref:
A.Ramos et al. (2000). RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J, 19, 997. PubMed id: 10698941 DOI: 10.1093/emboj/19.5.997
Date:
11-Mar-00     Release date:   21-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25159  (STAU_DROME) -  Maternal effect protein staufen
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1026 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biochemical function     RNA binding     2 terms  

 

 
DOI no: 10.1093/emboj/19.5.997 EMBO J 19:997 (2000)
PubMed id: 10698941  
 
 
RNA recognition by a Staufen double-stranded RNA-binding domain.
A.Ramos, S.Grünert, J.Adams, D.R.Micklem, M.R.Proctor, S.Freund, M.Bycroft, D.St Johnston, G.Varani.
 
  ABSTRACT  
 
The double-stranded RNA-binding domain (dsRBD) is a common RNA-binding motif found in many proteins involved in RNA maturation and localization. To determine how this domain recognizes RNA, we have studied the third dsRBD from Drosophila Staufen. The domain binds optimally to RNA stem-loops containing 12 uninterrupted base pairs, and we have identified the amino acids required for this interaction. By mutating these residues in a staufen transgene, we show that the RNA-binding activity of dsRBD3 is required in vivo for Staufen-dependent localization of bicoid and oskar mRNAs. Using high-resolution NMR, we have determined the structure of the complex between dsRBD3 and an RNA stem-loop. The dsRBD recognizes the shape of A-form dsRNA through interactions between conserved residues within loop 2 and the minor groove, and between loop 4 and the phosphodiester backbone across the adjacent major groove. In addition, helix alpha1 interacts with the single-stranded loop that caps the RNA helix. Interactions between helix alpha1 and single-stranded RNA may be important determinants of the specificity of dsRBD proteins.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Heteronuclear ^1H-^15N NOE for free (A) and RNA-bound (B) Staufen dsRBD3. 		Figure 6.
Figure 6 Intermolecular interactions between dsRBD and the RNA stem–loop in the superposition of 10 converged structures; one structure is represented in orange for clarity. (A) Interaction between loop 2 and the minor groove of the double-helical stem; Ala27 and His28 from the conserved GPAH sequence and the Lys30 side chains are shown explicitly; 2'-OH groups in close proximity to amino acids side chains are highlighted in red. (B) Interactions between loop 4 and the N-terminus of helix 2 and RNA phosphates (in red). (C) Interaction between helix 1 and the UUCG tetraloop.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 997-0) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Global analysis of non-specific protein-nucleic interactions by sedimentation equilibrium.
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Secondary structures common to chloroplast mRNA 3'-untranslated regions direct cleavage by CSP41, an endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily.
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PDB codes: 1k4a 1k4b
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PDB codes: 1k6g 1k6h
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Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage.
  Structure, 9, 1225-1236.
PDB codes: 1i4s 1jfz
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Recent advances in RNA-protein recognition.
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Mechanism of activation of the double-stranded-RNA-dependent protein kinase, PKR: role of dimerization and cellular localization in the stimulation of PKR phosphorylation of eukaryotic initiation factor-2 (eIF2).
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Solution structure of HI0257, a bacterial ribosome binding protein.
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PDB code: 1imu
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Translational regulation and RNA localization in Drosophila oocytes and embryos.
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Selective binding by the RNA binding domain of PKR revealed by affinity cleavage.
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The RNA-binding protein Tsunagi interacts with Mago Nashi to establish polarity and localize oskar mRNA during Drosophila oogenesis.
  Genes Dev, 15, 2886-2899.  
10716936 D.R.Micklem, J.Adams, S.Grünert, and D.St Johnston (2000).
Distinct roles of two conserved Staufen domains in oskar mRNA localization and translation.
  EMBO J, 19, 1366-1377.  
11118222 F.H.Allain, P.Bouvet, T.Dieckmann, and J.Feigon (2000).
Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin.
  EMBO J, 19, 6870-6881.
PDB code: 1fje
  10980424 H.D.Lipshitz, and C.A.Smibert (2000).
Mechanisms of RNA localization and translational regulation.
  Curr Opin Genet Dev, 10, 476-488.  
  10980425 J.A.Fischer (2000).
Molecular motors and developmental asymmetry.
  Curr Opin Genet Dev, 10, 489-496.  
11032824 S.Nanduri, F.Rahman, B.R.Williams, and J.Qin (2000).
A dynamically tuned double-stranded RNA binding mechanism for the activation of antiviral kinase PKR.
  EMBO J, 19, 5567-5574.  
11114159 X.Zheng, and P.C.Bevilacqua (2000).
Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR.
  Proc Natl Acad Sci U S A, 97, 14162-14167.  
11295750 A.Ramos, P.Bayer, and G.Varani (1999).
Determination of the structure of the RNA complex of a double-stranded RNA-binding domain from Drosophila Staufen protein.
  Biopolymers, 52, 181-196.  
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