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PDBsum entry 1e8o
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protein dna_rna ligands Protein-protein interface(s) links
Alu ribonucleoprotein particle PDB id
1e8o

 

 

 

 

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Contents
Protein chains
74 a.a. *
75 a.a. *
76 a.a. *
DNA/RNA
Ligands
SO4 ×3
Waters ×22
* Residue conservation analysis
PDB id:
1e8o
Name: Alu ribonucleoprotein particle
Title: Core of the alu domain of the mammalian srp
Structure: Signal recognition particle 9 kda protein. Chain: a, c. Synonym: srp9. Engineered: yes. Signal recognition particle 14 kda protein. Chain: b, d. Fragment: truncated after k107. Synonym: srp14. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: cytoplasm, nucleus?. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the RNA was produced by in vitro transcription with t7 RNA polymerase using ribozyme technology.
Biol. unit: Decamer (from PQS)
Resolution:
3.20Å     R-factor:   0.245     R-free:   0.291
Authors: O.Weichenrieder,K.Wild,K.Strub,S.Cusack
Key ref:
O.Weichenrieder et al. (2000). Structure and assembly of the Alu domain of the mammalian signal recognition particle. Nature, 408, 167-173. PubMed id: 11089964 DOI: 10.1038/35041507
Date:
28-Sep-00     Release date:   08-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P49458  (SRP09_HUMAN) -  Signal recognition particle 9 kDa protein from Homo sapiens
Seq:
Struc: 		86 a.a.
74 a.a.
Protein chain
P37108  (SRP14_HUMAN) -  Signal recognition particle 14 kDa protein from Homo sapiens
Seq:
Struc: 		136 a.a.
75 a.a.
Protein chain
P37108  (SRP14_HUMAN) -  Signal recognition particle 14 kDa protein from Homo sapiens
Seq:
Struc: 		136 a.a.
76 a.a.
Key:    Secondary structure  CATH domain

DNA/RNA chain
  GDP-G-G-C-C-G-G-G-C-G-C-G-G-U-G-G-C-G-C-G-C-G-C-C-U-G-U-A-G-U-C-C-C-A-G-C-U-A- 50 bases

 

 
DOI no: 10.1038/35041507 Nature 408:167-173 (2000)
PubMed id: 11089964  
 
 
Structure and assembly of the Alu domain of the mammalian signal recognition particle.
O.Weichenrieder, K.Wild, K.Strub, S.Cusack.
 
  ABSTRACT  
 
The Alu domain of the mammalian signal recognition particle (SRP) comprises the heterodimer of proteins SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. It retards the ribosomal elongation of signal-peptide-containing proteins before their engagement with the translocation machinery in the endoplasmic reticulum. Here we report two crystal structures of the heterodimer SRP9/14 bound either to the 5' domain or to a construct containing both 5' and 3' domains. We present a model of the complete Alu domain that is consistent with extensive biochemical data. SRP9/14 binds strongly to the conserved core of the 5' domain, which forms a U-turn connecting two helical stacks. Reversible docking of the more weakly bound 3' domain might be functionally important in the mechanism of translational regulation. The Alu domain structure is probably conserved in other cytoplasmic ribonucleoprotein particles and retroposition intermediates containing SRP9/14-bound RNAs transcribed from Alu repeats or related elements in genomic DNA.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Mammalian SRP and Alu domain RNA constructs. a, Mammalian SRP with SRP RNA bound to six proteins. The Alu domain is coloured red (SRP9), green (SRP14), blue (Alu RNA 5' domain) and cyan (Alu RNA 3' domain). b, SA86, the minimal Alu RNA folding domain. S-domain RNA is replaced by a GUAA tetraloop (grey). The green arrow indicates flexibility between the RNA 5' and 3' domains. Hydroxyl-radical footprints of SRP9/14 on SRP RNA are highlighted in magenta^21. c, SA88, a circular permutation of SA86. The original 5' and 3' ends are connected by a mono-uridine linker (black), constraining the RNA 5' and 3' domains to stack in an extended conformation (red bar). The GUAA tetraloop is replaced by a terminal stem (grey). The asymmetric internal loop is highlighted (yellow). 		Figure 5.
Figure 5: Structure of the Alu domain of the mammalian SRP (see Fig. 1 for colours). a, The SA88 Alu RNP with the alternative conformation of loop L1.2 in the SA50 Alu RNP in orange and the two europium sites in magenta. The disordered SRP14 1- 2 loop is indicated by a dotted line; helix H3.2 is coloured yellow; H, helix; L, loop. b, The SA88 Alu RNP dimer viewed down its crystallographic two-fold axis. c, Model for an Alu RNP (SA86) in its fully folded, physiological conformation with hydroxyl-radical footprints of SRP9/14 on SRP RNA^ 21 in magenta. d, As c, viewed down the SRP9/14 -sheet and illustrating the coverage of the previously exposed SRP9 surface with cysteines in yellow ball-and-stick representation.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 408, 167-173) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19609608 A.Tawfik Amin, N.Shiraishi, S.Ninomiya, M.Tajima, M.Inomata, and S.Kitano (2010).
Activation of nuclear factor kappa B and induction of migration inhibitory factor in tumors by surgical stress of laparotomy versus carbon dioxide pneumoperitoneum: an animal experiment.
  Surg Endosc, 24, 578-583.  
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.  
  20672053 C.Zwieb, and S.Bhuiyan (2010).
Archaea signal recognition particle shows the way.
  Archaea, 2010, 485051.  
20416380 D.C.Hancks, and H.H.Kazazian (2010).
SVA retrotransposons: Evolution and genetic instability.
  Semin Cancer Biol, 20, 234-245.  
21073748 E.Iakhiaeva, A.Iakhiaev, and C.Zwieb (2010).
Identification of amino acid residues in protein SRP72 required for binding to a kinked 5e motif of the human signal recognition particle RNA.
  BMC Mol Biol, 11, 83.  
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
19652014 A.Damert, J.Raiz, A.V.Horn, J.Löwer, H.Wang, J.Xing, M.A.Batzer, R.Löwer, and G.G.Schumann (2009).
5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome.
  Genome Res, 19, 1992-2008.  
19693936 E.Iakhiaeva, C.S.Hinck, A.P.Hinck, and C.Zwieb (2009).
Characterization of the SRP68/72 interface of human signal recognition particle by systematic site-directed mutagenesis.
  Protein Sci, 18, 2183-2195.  
19139409 E.Khazina, and O.Weichenrieder (2009).
Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame.
  Proc Natl Acad Sci U S A, 106, 731-736.
PDB code: 2w7a
19485416 G.Chen, S.D.Kennedy, and D.H.Turner (2009).
A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.
  Biochemistry, 48, 5738-5752.  
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
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.  
19240333 R.F.Fischetti, S.Xu, D.W.Yoder, M.Becker, V.Nagarajan, R.Sanishvili, M.C.Hilgart, S.Stepanov, O.Makarov, and J.L.Smith (2009).
Mini-beam collimator enables microcrystallography experiments on standard beamlines.
  J Synchrotron Radiat, 16, 217-225.  
18455985 A.K.Lakkaraju, C.Mary, A.Scherrer, A.E.Johnson, and K.Strub (2008).
SRP keeps polypeptides translocation-competent by slowing translation to match limiting ER-targeting sites.
  Cell, 133, 440-451.  
  18597676 D.Bach, S.Peddi, B.Mangeat, A.Lakkaraju, K.Strub, and D.Trono (2008).
Characterization of APOBEC3G binding to 7SL RNA.
  Retrovirology, 5, 54.  
18836035 E.A.Bennett, H.Keller, R.E.Mills, S.Schmidt, J.V.Moran, O.Weichenrieder, and S.E.Devine (2008).
Active Alu retrotransposons in the human genome.
  Genome Res, 18, 1875-1883.  
18441046 E.Iakhiaeva, J.Wower, I.K.Wower, and C.Zwieb (2008).
The 5e motif of eukaryotic signal recognition particle RNA contains a conserved adenosine for the binding of SRP72.
  RNA, 14, 1143-1153.  
18549262 J.H.Rho, S.Qin, J.Y.Wang, and M.H.Roehrl (2008).
Proteomic expression analysis of surgical human colorectal cancer tissues: up-regulation of PSB7, PRDX1, and SRP9 and hypoxic adaptation in cancer.
  J Proteome Res, 7, 2959-2972.  
18391409 R.Sanishvili, V.Nagarajan, D.Yoder, M.Becker, S.Xu, S.Corcoran, D.L.Akey, J.L.Smith, and R.F.Fischetti (2008).
A 7 microm mini-beam improves diffraction data from small or imperfect crystals of macromolecules.
  Acta Crystallogr D Biol Crystallogr, 64, 425-435.  
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17175535 T.Khanam, T.S.Rozhdestvensky, M.Bundman, C.R.Galiveti, S.Handel, V.Sukonina, U.Jordan, J.Brosius, and B.V.Skryabin (2007).
Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners.
  Nucleic Acids Res, 35, 529-539.  
16373494 A.Lescoute, and E.Westhof (2006).
Topology of three-way junctions in folded RNAs.
  RNA, 12, 83-93.  
16672232 E.Iakhiaeva, S.H.Bhuiyan, J.Yin, and C.Zwieb (2006).
Protein SRP68 of human signal recognition particle: identification of the RNA and SRP72 binding domains.
  Protein Sci, 15, 1290-1302.  
16682445 J.Häsler, and K.Strub (2006).
Alu RNP and Alu RNA regulate translation initiation in vitro.
  Nucleic Acids Res, 34, 2374-2385.  
17020921 J.Häsler, and K.Strub (2006).
Alu elements as regulators of gene expression.
  Nucleic Acids Res, 34, 5491-5497.  
15611297 C.Zwieb, R.W.van Nues, M.A.Rosenblad, J.D.Brown, and T.Samuelsson (2005).
A nomenclature for all signal recognition particle RNAs.
  RNA, 11, 7.  
16153164 M.Pohlschröder, E.Hartmann, N.J.Hand, K.Dilks, and A.Haddad (2005).
Diversity and evolution of protein translocation.
  Annu Rev Microbiol, 59, 91.  
15189152 J.A.Doudna, and R.T.Batey (2004).
Structural insights into the signal recognition particle.
  Annu Rev Biochem, 73, 539-557.  
15228518 K.Wild, K.R.Rosendal, and I.Sinning (2004).
A structural step into the SRP cycle.
  Mol Microbiol, 53, 357-363.  
15383645 L.Huck, A.Scherrer, L.Terzi, A.E.Johnson, H.D.Bernstein, S.Cusack, O.Weichenrieder, and K.Strub (2004).
Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain.
  Nucleic Acids Res, 32, 4915-4924.  
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.  
14985753 M.Halic, T.Becker, M.R.Pool, C.M.Spahn, R.A.Grassucci, J.Frank, and R.Beckmann (2004).
Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
  Nature, 427, 808-814.
PDB code: 1ry1
15274918 O.Weichenrieder, K.Repanas, and A.Perrakis (2004).
Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.
  Structure, 12, 975-986.
PDB code: 1vyb
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
15186764 S.Rospert (2004).
Ribosome function: governing the fate of a nascent polypeptide.
  Curr Biol, 14, R386-R388.  
12581661 A.E.Sauer-Eriksson, and T.Hainzl (2003).
S-domain assembly of the signal recognition particle.
  Curr Opin Struct Biol, 13, 64-70.  
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.  
12606550 L.Liu, H.Ben-Shlomo, Y.X.Xu, M.Z.Stern, I.Goncharov, Y.Zhang, and S.Michaeli (2003).
The trypanosomatid signal recognition particle consists of two RNA molecules, a 7SL RNA homologue and a novel tRNA-like molecule.
  J Biol Chem, 278, 18271-18280.  
14532128 M.De la Peña, S.Gago, and R.Flores (2003).
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity.
  EMBO J, 22, 5561-5570.  
12796500 M.T.Nguyen, J.Beck, H.Lue, H.Fünfzig, R.Kleemann, P.Koolwijk, A.Kapurniotu, and J.Bernhagen (2003).
A 16-residue peptide fragment of macrophage migration inhibitory factor, MIF-(50-65), exhibits redox activity and has MIF-like biological functions.
  J Biol Chem, 278, 33654-33671.  
12736311 T.Leeper, N.Leulliot, and G.Varani (2003).
The solution structure of an essential stem-loop of human telomerase RNA.
  Nucleic Acids Res, 31, 2614-2621.
PDB code: 1oq0
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
  15803656 C.Zwieb, and J.Eichler (2002).
Getting on target: the archaeal signal recognition particle.
  Archaea, 1, 27-34.  
12364595 I.Tozik, Q.Huang, C.Zwieb, and J.Eichler (2002).
Reconstitution of the signal recognition particle of the halophilic archaeon Haloferax volcanii.
  Nucleic Acids Res, 30, 4166-4175.  
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.  
12140321 M.Regalia, M.A.Rosenblad, and T.Samuelsson (2002).
Prediction of signal recognition particle RNA genes.
  Nucleic Acids Res, 30, 3368-3377.  
12050674 T.Hainzl, S.Huang, and A.E.Sauer-Eriksson (2002).
Structure of the SRP19 RNA complex and implications for signal recognition particle assembly.
  Nature, 417, 767-771.
PDB code: 1lng
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.  
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.  
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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