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PDBsum entry 1cql
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RNA PDB id
1cql

 

 

 

 

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Contents
DNA/RNA
PDB id:
1cql
Name: RNA
Title: Nmr structure of srp RNA domain iv
Structure: Srp domain iv RNA. Chain: a. Fragment: modified e. Coli sequence. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
NMR struc: 10 models
Authors: U.Schmitz,T.L.James
Key ref: U.Schmitz et al. (1999). Structure of the phylogenetically most conserved domain of SRP RNA. Rna, 5, 1419-1429. PubMed id: 10580470
Date:
06-Aug-99     Release date:   14-Jan-00    
 Headers
 References

DNA/RNA chain
  G-G-C-G-U-U-U-A-C-C-A-G-G-U-C-A-G-G-U-C-C-G-G-A-A-G-G-A-A-G-C-A-G-C-C-A-A-G-G- 43 bases

 

 
Rna 5:1419-1429 (1999)
PubMed id: 10580470  
 
 
Structure of the phylogenetically most conserved domain of SRP RNA.
U.Schmitz, S.Behrens, D.M.Freymann, R.J.Keenan, P.Lukavsky, P.Walter, T.L.James.
 
  ABSTRACT  
 
The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein required for cotranslational targeting of proteins to the membrane of the endoplasmic reticulum of the bacterial plasma membrane. Domain IV of SRP RNA consists of a short stem-loop structure with two internal loops that contain the most conserved nucleotides of the molecule. All known essential interactions of SRP occur in that moiety containing domain IV. The solution structure of a 43-nt RNA comprising the complete Escherichia coli domain IV was determined by multidimensional NMR and restrained molecular dynamics refinement. Our data confirm the previously determined rigid structure of a smaller subfragment containing the most conserved, symmetric internal loop A (Schmitz et al., Nat Struct Biol, 1999, 6:634-638), where all conserved nucleotides are involved in nucleotide-specific structural interactions. Asymmetric internal loop B provides a hinge in the RNA molecule; it is partially flexible, yet also uniquely structured. The longer strand of internal loop B extends the major groove by creating a ledge-like arrangement; for loop B however, there is no obvious structural role for the conserved nucleotides. The structure of domain IV suggests that loop A is the initial site for the RNA/protein interaction creating specificity, whereas loop B provides a secondary interaction site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179341 K.Wild, G.Bange, G.Bozkurt, B.Segnitz, A.Hendricks, and I.Sinning (2010).
Structural insights into the assembly of the human and archaeal signal recognition particles.
  Acta Crystallogr D Biol Crystallogr, 66, 295-303.
PDB codes: 3ktv 3ktw
19741022 M.de la Peña, D.Dufour, and J.Gallego (2009).
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold.
  RNA, 15, 1949-1964.  
18281388 S.Fulle, and H.Gohlke (2008).
Analyzing the flexibility of RNA structures by constraint counting.
  Biophys J, 94, 4202-4219.  
16333319 C.V.Nicchitta, R.S.Lerner, S.B.Stephens, R.D.Dodd, and B.Pyhtila (2005).
Pathways for compartmentalizing protein synthesis in eukaryotic cells: the template-partitioning model.
  Biochem Cell Biol, 83, 687-695.  
15928341 T.Hainzl, S.Huang, and A.E.Sauer-Eriksson (2005).
Structural insights into SRP RNA: an induced fit mechanism for SRP assembly.
  RNA, 11, 1043-1050.
PDB code: 1z43
15100432 M.B.Sagar, L.Lucast, and J.A.Doudna (2004).
Conserved but nonessential interaction of SRP RNA with translation factor EF-G.
  RNA, 10, 772-778.  
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
15273327 S.Baba, M.Kajikawa, N.Okada, and G.Kawai (2004).
Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2.
  RNA, 10, 1380-1387.
PDB code: 1wks
12581661 A.E.Sauer-Eriksson, and T.Hainzl (2003).
S-domain assembly of the signal recognition particle.
  Curr Opin Struct Biol, 13, 64-70.  
12777762 J.Deng, Y.Xiong, B.Pan, and M.Sundaralingam (2003).
Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 1004-1011.
PDB code: 1lnt
12853463 K.Nagai, C.Oubridge, A.Kuglstatter, E.Menichelli, C.Isel, and L.Jovine (2003).
Structure, function and evolution of the signal recognition particle.
  EMBO J, 22, 3479-3485.  
14500816 S.Matsumura, Y.Ikawa, and T.Inoue (2003).
Biochemical characterization of the kink-turn RNA motif.
  Nucleic Acids Res, 31, 5544-5551.  
12244299 A.Kuglstatter, C.Oubridge, and K.Nagai (2002).
Induced structural changes of 7SL RNA during the assembly of human signal recognition particle.
  Nat Struct Biol, 9, 740-744.
PDB code: 1mfq
12086622 C.Oubridge, A.Kuglstatter, L.Jovine, and K.Nagai (2002).
Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle.
  Mol Cell, 9, 1251-1261.
PDB code: 1l9a
12466557 G.B.Fogel, V.W.Porto, D.G.Weekes, D.B.Fogel, R.H.Griffey, J.A.McNeil, E.Lesnik, D.J.Ecker, and R.Sampath (2002).
Discovery of RNA structural elements using evolutionary computation.
  Nucleic Acids Res, 30, 5310-5317.  
11233986 J.R.Jagath, N.B.Matassova, E.de Leeuw, J.M.Warnecke, G.Lentzen, M.V.Rodnina, J.Luirink, and W.Wintermeyer (2001).
Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY.
  RNA, 7, 293-301.  
11395422 R.J.Keenan, D.M.Freymann, R.M.Stroud, and P.Walter (2001).
The signal recognition particle.
  Annu Rev Biochem, 70, 755-775.  
11713323 T.J.Macke, D.J.Ecker, R.R.Gutell, D.Gautheret, D.A.Case, and R.Sampath (2001).
RNAMotif, an RNA secondary structure definition and search algorithm.
  Nucleic Acids Res, 29, 4724-4735.  
11041851 J.L.Diener, and C.Wilson (2000).
Role of SRP19 in assembly of the Archaeoglobus fulgidus signal recognition particle.
  Biochemistry, 39, 12862-12874.  
10944346 L.Jovine, T.Hainz, C.Oubridge, and K.Nagai (2000).
Crystallization and preliminary X-ray analysis of the conserved domain IV of Escherichia coli 4.5S RNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1033-1037.  
10801497 L.Jovine, T.Hainzl, C.Oubridge, W.G.Scott, J.Li, T.K.Sixma, A.Wonacott, T.Skarzynski, and K.Nagai (2000).
Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.
  Structure, 8, 527-540.
PDB code: 1duh
10896472 P.B.Rupert, and A.R.Ferré-D'amaré (2000).
SRPrises in RNA-protein recognition.
  Structure, 8, R99-104.  
10607673 R.M.Stroud, and P.Walter (1999).
Signal sequence recognition and protein targeting.
  Curr Opin Struct Biol, 9, 754-759.  
11295748 S.J.Schroeder, M.E.Burkard, and D.H.Turner (1999).
The energetics of small internal loops in RNA.
  Biopolymers, 52, 157-167.  
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 codes are shown on the right.

 

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