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PDBsum entry 1914

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Alu domain PDB id
1914
Jmol
Contents
Protein chain
171 a.a.
Ligands
PO4
BME
Waters ×17
PDB id:
1914
Name: Alu domain
Title: Signal recognition particle alu RNA binding heterodimer, srp
Structure: Signal recognition particle 9/14 fusion protein. Chain: a. Fragment: alu RNA binding heterodimer. Synonym: srp9/14, alu bm, rbd. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: bl21 plyss. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.53Å     R-factor:   0.248     R-free:   0.299
Authors: D.Birse,U.Kapp,K.Strub,S.Cusack,A.Aberg
Key ref:
D.E.Birse et al. (1997). The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14. EMBO J, 16, 3757-3766. PubMed id: 9233785 DOI: 10.1093/emboj/16.13.3757
Date:
13-Nov-97     Release date:   30-Dec-98    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16254  (SRP14_MOUSE) -  Signal recognition particle 14 kDa protein
Seq:
Struc:
110 a.a.
171 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intercellular bridge   8 terms 
  Biological process     response to drug   3 terms 
  Biochemical function     RNA binding     4 terms  

 

 
DOI no: 10.1093/emboj/16.13.3757 EMBO J 16:3757-3766 (1997)
PubMed id: 9233785  
 
 
The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14.
D.E.Birse, U.Kapp, K.Strub, S.Cusack, A.Aberg.
 
  ABSTRACT  
 
The mammalian signal recognition particle (SRP) is an 11S cytoplasmic ribonucleoprotein that plays an essential role in protein sorting. SRP recognizes the signal sequence of the nascent polypeptide chain emerging from the ribosome, and targets the ribosome-nascent chain-SRP complex to the rough endoplasmic reticulum. The SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide RNA molecule. SRP9 and SRP14 proteins form a heterodimer that binds to the Alu domain of SRP RNA which is responsible for translation arrest. We report the first crystal structure of a mammalian SRP protein, that of the mouse SRP9/14 heterodimer, determined at 2.5 A resolution. SRP9 and SRP14 are found to be structurally homologous, containing the same alpha-beta-beta-beta-alpha fold. This we designate the Alu binding module (Alu bm), an additional member of the family of small alpha/beta RNA binding domains. The heterodimer has pseudo 2-fold symmetry and is saddle like, comprising a strongly curved six-stranded amphipathic beta-sheet with the four helices packed on the convex side and the exposed concave surface being lined with positively charged residues.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 (A) Stereo diagram of the SRP9/14 heterodimer, viewed looking onto the -sheet surface, showing secondary structure elements. Basic residues which project out of the -sheet surface are depicted with their side chains (SRP9-Arg26, SRP9-Lys30, SRP9-Arg32, SRP9-Lys41, SRP9-Arg52, SRP14-Lys31, SRP14-Lys55, SRP14-Arg59, SRP14-Lys66 and loop residues SRP9-Lys24 and SRP14-Lys74). Also shown is residue SRP14-Phe27 protruding out from the -sheet surface and two cysteines (SRP9-Cys39 and SRP9-Cys48) implicated in NEM studies of SRP9. The blue strand represents a region of the fusion linker which may displace a putative SRP9 N-terminal parallel -strand. Diagrams were made using the program MOLSCRIPT (Kraulis, 1991) and RASTER3D (Merritt and Murphy, 1994). (B) A side view of the SRP9/14 heterodimer superimposed with a helical RNA molecule. The curvature of the -sheet conforms to that of the RNA (modelled with a six based-paired double-stranded helical region of tRNA).
Figure 5.
Figure 5 (A) Stereo diagram of electron density representation of solvent-flattened experimental MIR maps contoured at 1.0 (in white) and difference Fourier maps of selenomethionine density (in red) with stick-model of SRP9/14 heterodimer. The difference Fourier map for selenomethionine density was calculated using MIR phases from mercury and platinum contoured at 6.0 . Methionine sites shown (SRP9-Met23, SRP9-Met73, SRP9-Met70 and SRP14-Met91) of the model superimpose with selenomethionine density. (B) Stereo diagram of 2F[obs] -F[calc] electron density maps with the refined model contoured at 1.2 showing the hydrogen bond between SRP9-His66 and SRP14-Tyr83 within the hydrophobic core of the SRP9/14 molecule.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 3757-3766) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20348448 C.Mary, A.Scherrer, L.Huck, A.K.Lakkaraju, Y.Thomas, A.E.Johnson, and K.Strub (2010).
Residues in SRP9/14 essential for elongation arrest activity of the signal recognition particle define a positively charged functional domain on one side of the protein.
  RNA, 16, 969-979.  
19390147 M.A.Brooks, R.B.Ravelli, A.A.McCarthy, K.Strub, and S.Cusack (2009).
Structure of SRP14 from the Schizosaccharomyces pombe signal recognition particle.
  Acta Crystallogr D Biol Crystallogr, 65, 421-433.
PDB code: 2w9j
15112237 E.Staub, P.Fiziev, A.Rosenthal, and B.Hinzmann (2004).
Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.
  Bioessays, 26, 567-581.  
15228518 K.Wild, K.R.Rosendal, and I.Sinning (2004).
A structural step into the SRP cycle.
  Mol Microbiol, 53, 357-363.  
15502345 K.Yamane, K.Bunai, and H.Kakeshita (2004).
Protein traffic for secretion and related machinery of Bacillus subtilis.
  Biosci Biotechnol Biochem, 68, 2007-2023.  
14720308 M.A.Rosenblad, C.Zwieb, and T.Samuelsson (2004).
Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi.
  BMC Genomics, 5, 5.  
15048814 S.Hovmöller, and T.Zhou (2004).
Why are both ends of the polypeptide chain on the outside of proteins?
  Proteins, 55, 219-222.  
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.  
12011081 J.H.Bayle, F.Randazzo, G.Johnen, S.Kaufman, A.Nagy, J.Rossant, and G.R.Crabtree (2002).
Hyperphenylalaninemia and impaired glucose tolerance in mice lacking the bifunctional DCoH gene.
  J Biol Chem, 277, 28884-28891.  
11839493 K.Wild, O.Weichenrieder, K.Strub, I.Sinning, and S.Cusack (2002).
Towards the structure of the mammalian signal recognition particle.
  Curr Opin Struct Biol, 12, 72-81.  
11567158 A.Perrakis, M.Harkiolaki, K.S.Wilson, and V.S.Lamzin (2001).
ARP/wARP and molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 57, 1445-1450.  
11239791 J.Eichler, and R.Moll (2001).
The signal recognition particle of Archaea.
  Trends Microbiol, 9, 130-136.  
11641499 K.Wild, I.Sinning, and S.Cusack (2001).
Crystal structure of an early protein-RNA assembly complex of the signal recognition particle.
  Science, 294, 598-601.
PDB code: 1jid
11350037 O.Weichenrieder, C.Stehlin, U.Kapp, D.E.Birse, P.A.Timmins, K.Strub, and S.Cusack (2001).
Hierarchical assembly of the Alu domain of the mammalian signal recognition particle.
  RNA, 7, 731-740.  
11395422 R.J.Keenan, D.M.Freymann, R.M.Stroud, and P.Walter (2001).
The signal recognition particle.
  Annu Rev Biochem, 70, 755-775.  
  11206077 M.Teplova, V.Tereshko, R.Sanishvili, A.Joachimiak, T.Bushueva, W.F.Anderson, and M.Egli (2000).
The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding.
  Protein Sci, 9, 2557-2566.
PDB code: 1hru
10921896 N.Mason, L.F.Ciufo, and J.D.Brown (2000).
Elongation arrest is a physiologically important function of signal recognition particle.
  EMBO J, 19, 4164-4174.  
10684931 S.H.Bhuiyan, K.Gowda, H.Hotokezaka, and C.Zwieb (2000).
Assembly of archaeal signal recognition particle from recombinant components.
  Nucleic Acids Res, 28, 1365-1373.  
10224127 K.Nakamura, S.Yahagi, T.Yamazaki, and K.Yamane (1999).
Bacillus subtilis histone-like protein, HBsu, is an integral component of a SRP-like particle that can bind the Alu domain of small cytoplasmic RNA.
  J Biol Chem, 274, 13569-13576.  
10521474 K.Sinha, K.Perumal, Y.Chen, and R.Reddy (1999).
Post-transcriptional adenylation of signal recognition particle RNA is carried out by an enzyme different from mRNA Poly(A) polymerase.
  J Biol Chem, 274, 30826-30831.  
10573124 K.Strub, M.Fornallaz, and N.Bui (1999).
The Alu domain homolog of the yeast signal recognition particle consists of an Srp14p homodimer and a yeast-specific RNA structure.
  RNA, 5, 1333-1347.  
10574798 K.Wild, O.Weichenrieder, G.A.Leonard, and S.Cusack (1999).
The 2 A structure of helix 6 of the human signal recognition particle RNA.
  Structure, 7, 1345-1352.
PDB code: 1d4r
10195420 N.Bui, and K.Strub (1999).
New insights into signal recognition and elongation arrest activities of the signal recognition particle.
  Biol Chem, 380, 135-145.  
10400475 S.Cusack (1999).
RNA-protein complexes.
  Curr Opin Struct Biol, 9, 66-73.  
9857035 Y.Chen, K.Sinha, K.Perumal, J.Gu, and R.Reddy (1998).
Accurate 3' end processing and adenylation of human signal recognition particle RNA and alu RNA in vitro.
  J Biol Chem, 273, 35023-35031.  
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.