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PDBsum entry 2j37

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
2j37
Jmol
Contents
Protein chains
81 a.a. *
64 a.a. *
81 a.a. *
107 a.a. *
17 a.a. *
479 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
2j37
Name: Ribosome
Title: Model of mammalian srp bound to 80s rncs
Structure: Signal recognition particle 19 kda protein (srp19). Chain: b. Signal recognition particle 54 kda protein (srp54). Chain: w. Signal sequence. Chain: s. Ribosomal protein l35.
Source: Homo sapiens. Human. Organism_taxid: 9606. Canis sp.. Organism_taxid: 9616. Synthetic: yes. Triticum sp.. Wheat. Organism_taxid: 4569.
Biol. unit: Octamer (from PDB file)
Authors: M.Halic,M.Blau,T.Becker,T.Mielke,M.R.Pool,K.Wild,I.Sinning, R.Beckmann
Key ref:
M.Halic et al. (2006). Following the signal sequence from ribosomal tunnel exit to signal recognition particle. Nature, 444, 507-511. PubMed id: 17086193 DOI: 10.1038/nature05326
Date:
18-Aug-06     Release date:   08-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O81229  (O81229_MAIZE) -  Ribosomal protein L25 (Fragment)
Seq:
Struc:
109 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
Q8L805  (RL35_WHEAT) -  60S ribosomal protein L35
Seq:
Struc:
124 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
Q5XLD9  (Q5XLD9_MAIZE) -  Putative 60S ribosomal protein L31
Seq:
Struc:
124 a.a.
81 a.a.*
Protein chain
Pfam   ArchSchema ?
P09132  (SRP19_HUMAN) -  Signal recognition particle 19 kDa protein
Seq:
Struc:
144 a.a.
107 a.a.
Protein chain
Pfam   ArchSchema ?
Q1WHN3  (Q1WHN3_ALLSI) -  Rhodopsin (Fragment)
Seq:
Struc:
105 a.a.
17 a.a.
Protein chain
Pfam   ArchSchema ?
P61010  (SRP54_CANFA) -  Signal recognition particle 54 kDa protein
Seq:
Struc:
504 a.a.
479 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   9 terms 
  Biological process     response to drug   7 terms 
  Biochemical function     nucleotide binding     11 terms  

 

 
DOI no: 10.1038/nature05326 Nature 444:507-511 (2006)
PubMed id: 17086193  
 
 
Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
M.Halic, M.Blau, T.Becker, T.Mielke, M.R.Pool, K.Wild, I.Sinning, R.Beckmann.
 
  ABSTRACT  
 
Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Cryo-electron microscopic structure of programmed 70S ribosome (RNC) with signal sequence. a, Density map with the ribosomal 30S subunit shown in yellow, 50S in blue and the P-site tRNA and nascent chain (signal sequence) in green. Landmarks are indicated. CP, central protuberance. b, Section through the ribosome showing the signal sequence at the tunnel exit site. c, Comparison of the ribosomal tunnel exit site of 70S RNC (left) with the empty 70S ribosome (3D-EM database accession number EMD1055)^7 (right). Additional density (signal sequence) is shown in green. d, View as in c, with ribosomal density shown as a white mesh and models as ribbons. rRNA is shown in blue; L23p, L24p and L29p in magenta; signal sequence in green.
Figure 4.
Figure 4: Mammalian SRP bound to 80S RNC. a, Cryo-electron microscopic structure of the mammalian SRP bound to 80S wheat germ RNC. b, Density representing the hydrophobic groove of the SRP54 M domain with the signal sequence bound. c, Same view as in b showing the docked crystal structure of SRP54 M domain (red) and the signal sequence (green) docked into extra density. d, A model of the C-terminal part of SRP54 M domain is shown in purple docked into the additional density of SRP54 (left). SRP54 density is shown as a grey mesh, and the ribosome is shown in blue. e, Model of the fitted ribosome-bound mammalian NG domain. f, Top view of the four-helix bundle of the SRP54 N domain based on the monomeric NG domain in red (top), and superimposed on the N domain from the NG twin structure in yellow (bottom). g, Comparison of the model of ribosome-bound NG domain (red, NG ribo) with the monomeric unbound domain (blue, NG mono) and with the twin NG domain (yellow, NG twin). h, The complete model of mammalian SRP S domain (red). i, The E. coli model (red) superimposed on the mammalian model (white).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 444, 507-511) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23235881 K.Shen, S.Arslan, D.Akopian, T.Ha, and S.O.Shan (2012).
Activated GTPase movement on an RNA scaffold drives co-translational protein targeting.
  Nature, 492, 271-275.  
21316217 D.N.Wilson, and R.Beckmann (2011).
The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling.
  Curr Opin Struct Biol, 21, 274-282.  
21438832 D.Rolland, A.Bouamrani, R.Houlgatte, A.Barbarat, C.Ramus, M.Arlotto, B.Ballester, F.Berger, P.Felman, E.Callet-Bauchu, L.Baseggio, A.Traverse-Glehen, S.Brugière, J.Garin, B.Coiffier, F.Berger, and C.Thieblemont (2011).
Identification of proteomic signatures of mantle cell lymphoma, small lymphocytic lymphoma, and marginal zone lymphoma biopsies by surface enhanced laser desorption/ionization-time of flight mass spectrometry.
  Leuk Lymphoma, 52, 648-658.  
21291501 I.Saraogi, and S.O.Shan (2011).
Molecular mechanism of co-translational protein targeting by the signal recognition particle.
  Traffic, 12, 535-542.  
21499241 J.Frauenfeld, J.Gumbart, E.O.Sluis, S.Funes, M.Gartmann, B.Beatrix, T.Mielke, O.Berninghausen, T.Becker, K.Schulten, and R.Beckmann (2011).
Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
  Nat Struct Mol Biol, 18, 614-621.
PDB codes: 3j00 3j01
21151118 L.F.Estrozi, D.Boehringer, S.O.Shan, N.Ban, and C.Schaffitzel (2011).
Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor.
  Nat Struct Mol Biol, 18, 88-90.
PDB code: 2xkv
21267063 S.Bhushan, T.Hoffmann, B.Seidelt, J.Frauenfeld, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2011).
SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center.
  PLoS Biol, 9, e1000581.  
21330537 S.F.Ataide, N.Schmitz, K.Shen, A.Ke, S.O.Shan, J.A.Doudna, and N.Ban (2011).
The crystal structure of the signal recognition particle in complex with its receptor.
  Science, 331, 881-886.
PDB code: 2xxa
20364120 C.Y.Janda, J.Li, C.Oubridge, H.Hernández, C.V.Robinson, and K.Nagai (2010).
Recognition of a signal peptide by the signal recognition particle.
  Nature, 465, 507-510.
PDB code: 3kl4
  20714446 I.Yosef, E.S.Bochkareva, and E.Bibi (2010).
Escherichia coli SRP, Its Protein Subunit Ffh, and the Ffh M Domain Are Able To Selectively Limit Membrane Protein Expression When Overexpressed.
  MBio, 1, 0.  
20385832 K.Shen, and S.O.Shan (2010).
Transient tether between the SRP RNA and SRP receptor ensures efficient cargo delivery during cotranslational protein targeting.
  Proc Natl Acad Sci U S A, 107, 7698-7703.  
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
20139981 S.Bhushan, M.Gartmann, M.Halic, J.P.Armache, A.Jarasch, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2010).
alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
  Nat Struct Mol Biol, 17, 313-317.  
20448185 X.Zhang, R.Rashid, K.Wang, and S.O.Shan (2010).
Sequential checkpoints govern substrate selection during cotranslational protein targeting.
  Science, 328, 757-760.  
19361278 A.Kuhn (2009).
From the Sec complex to the membrane insertase YidC.
  Biol Chem, 390, 701-706.  
20004164 A.Matsumoto, and H.Ishida (2009).
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.
  Structure, 17, 1605-1613.  
19305415 B.C.Cross, I.Sinning, J.Luirink, and S.High (2009).
Delivering proteins for export from the cytosol.
  Nat Rev Mol Cell Biol, 10, 255-264.  
19647435 C.Giglione, S.Fieulaine, and T.Meinnel (2009).
Cotranslational processing mechanisms: towards a dynamic 3D model.
  Trends Biochem Sci, 34, 417-426.  
19280642 E.M.Clérico, A.SzymaƄska, and L.M.Gierasch (2009).
Exploring the interactions between signal sequences and E. coli SRP by two distinct and complementary crosslinking methods.
  Biopolymers, 92, 201-211.  
19491936 G.Kramer, D.Boehringer, N.Ban, and B.Bukau (2009).
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins.
  Nat Struct Mol Biol, 16, 589-597.  
19029307 I.A.Buskiewicz, J.Jöckel, M.V.Rodnina, and W.Wintermeyer (2009).
Conformation of the signal recognition particle in ribosomal targeting complexes.
  RNA, 15, 44-54.  
19558326 P.Grudnik, G.Bange, and I.Sinning (2009).
Protein targeting by the signal recognition particle.
  Biol Chem, 390, 775-782.  
19587121 P.Jaru-Ampornpan, T.X.Nguyen, and S.O.Shan (2009).
A distinct mechanism to achieve efficient signal recognition particle (SRP)-SRP receptor interaction by the chloroplast srp pathway.
  Mol Biol Cell, 20, 3965-3973.  
19469550 S.O.Shan, S.L.Schmid, and X.Zhang (2009).
Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases.
  Biochemistry, 48, 6696-6704.  
19174514 X.Zhang, C.Schaffitzel, N.Ban, and S.O.Shan (2009).
Multiple conformational switches in a GTPase complex control co-translational protein targeting.
  Proc Natl Acad Sci U S A, 106, 1754-1759.  
18492794 A.Loya, L.Pnueli, Y.Yosefzon, Y.Wexler, M.Ziv-Ukelson, and Y.Arava (2008).
The 3'-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein.
  RNA, 14, 1352-1365.  
17918185 E.M.Clérico, J.L.Maki, and L.M.Gierasch (2008).
Use of synthetic signal sequences to explore the protein export machinery.
  Biopolymers, 90, 307-319.  
18448667 J.A.Dalley, A.Selkirk, and M.R.Pool (2008).
Access to ribosomal protein Rpl25p by the signal recognition particle is required for efficient cotranslational translocation.
  Mol Biol Cell, 19, 2876-2884.  
18611385 J.F.Ménétret, R.S.Hegde, M.Aguiar, S.P.Gygi, E.Park, T.A.Rapoport, and C.W.Akey (2008).
Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.
  Structure, 16, 1126-1137.
PDB code: 3dkn
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.  
19079550 K.N.Rao, S.K.Burley, and S.Swaminathan (2008).
UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
  PLoS ONE, 3, e3903.
PDB codes: 2nrq 2nwu 2ogk 2pzz
18829863 K.Peisker, D.Braun, T.Wölfle, J.Hentschel, U.Fünfschilling, G.Fischer, A.Sickmann, and S.Rospert (2008).
Ribosome-associated complex binds to ribosomes in close proximity of Rpl31 at the exit of the polypeptide tunnel in yeast.
  Mol Biol Cell, 19, 5279-5288.  
18953414 P.F.Egea, J.Napetschnig, P.Walter, and R.M.Stroud (2008).
Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus.
  PLoS ONE, 3, e3528.
PDB codes: 3dlu 3dlv 3dm5
18946046 P.M.Petrone, C.D.Snow, D.Lucent, and V.S.Pande (2008).
Side-chain recognition and gating in the ribosome exit tunnel.
  Proc Natl Acad Sci U S A, 105, 16549-16554.  
18573071 S.H.White, and G.von Heijne (2008).
How translocons select transmembrane helices.
  Annu Rev Biophys, 37, 23-42.  
19180078 T.R.Shaikh, H.Gao, W.T.Baxter, F.J.Asturias, N.Boisset, A.Leith, and J.Frank (2008).
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
  Nat Protoc, 3, 1941-1974.  
17429433 C.de Duve (2007).
The origin of eukaryotes: a reappraisal.
  Nat Rev Genet, 8, 395-403.  
17699634 G.Bange, G.Petzold, K.Wild, R.O.Parlitz, and I.Sinning (2007).
The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP.
  Proc Natl Acad Sci U S A, 104, 13621-13625.
PDB codes: 2px0 2px3
18029258 G.Bange, K.Wild, and I.Sinning (2007).
Protein translocation: checkpoint role for SRP GTPase activation.
  Curr Biol, 17, R980-R982.  
17507650 N.Bradshaw, and P.Walter (2007).
The signal recognition particle (SRP) RNA links conformational changes in the SRP to protein targeting.
  Mol Biol Cell, 18, 2728-2734.  
17475780 P.Jaru-Ampornpan, S.Chandrasekar, and S.O.Shan (2007).
Efficient interaction between two GTPases allows the chloroplast SRP pathway to bypass the requirement for an SRP RNA.
  Mol Biol Cell, 18, 2636-2645.  
17676771 S.L.Rusch, and D.A.Kendall (2007).
Interactions that drive Sec-dependent bacterial protein transport.
  Biochemistry, 46, 9665-9673.  
18046402 T.A.Rapoport (2007).
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes.
  Nature, 450, 663-669.  
17846429 T.Hainzl, S.Huang, and A.E.Sauer-Eriksson (2007).
Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle.
  Proc Natl Acad Sci U S A, 104, 14911-14916.
PDB code: 2v3c
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.