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PDBsum entry 1qzx

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protein Protein-protein interface(s) links
Signaling protein PDB id
1qzx
Jmol
Contents
Protein chains
425 a.a. *
* Residue conservation analysis
PDB id:
1qzx
Name: Signaling protein
Title: Crystal structure of the complete core of archaeal srp and implications for inter-domain communication
Structure: Signal recognition 54 kda protein. Chain: a, b. Synonym: srp54. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Gene: srp54. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
4.00Å     R-factor:   0.313     R-free:   0.383
Authors: K.R.Rosendal,K.Wild,G.Montoya,I.Sinning
Key ref:
K.R.Rosendal et al. (2003). Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication. Proc Natl Acad Sci U S A, 100, 14701-14706. PubMed id: 14657338 DOI: 10.1073/pnas.2436132100
Date:
18-Sep-03     Release date:   18-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q97ZE7  (SRP54_SULSO) -  Signal recognition particle 54 kDa protein
Seq:
Struc:
447 a.a.
425 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonucleoprotein complex   3 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1073/pnas.2436132100 Proc Natl Acad Sci U S A 100:14701-14706 (2003)
PubMed id: 14657338  
 
 
Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication.
K.R.Rosendal, K.Wild, G.Montoya, I.Sinning.
 
  ABSTRACT  
 
Targeting of secretory and membrane proteins by the signal recognition particle (SRP) is evolutionarily conserved, and the multidomain protein SRP54 acts as the key player in SRP-mediated protein transport. Binding of a signal peptide to SRP54 at the ribosome is coordinated with GTP binding and subsequent complex formation with the SRP receptor. Because these functions are localized to distinct domains of SRP54, communication between them is essential. We report the crystal structures of SRP54 from the Archaeon Sulfolobus solfataricus with and without its cognate SRP RNA binding site (helix 8) at 4-A resolution. The two structures show the flexibility of the SRP core and the position of SRP54 relative to the RNA. A long linker helix connects the GTPase (G domain) with the signal peptide binding (M) domain, and a hydrophobic contact between the N and M domains relates the signal peptide binding site to the G domain. Hinge regions are identified in the linker between the G and M domains (292-LGMGD) and in the N-terminal part of the M domain, which allow for structural rearrangements within SRP54 upon signal peptide binding at the ribosome.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Superposition of SRP54 with (red) and without (blue) RNA shown as a ribbon diagram. The RNA is omitted for clarity. A rotation axis (green) has been identified between the N and M domains by the program DYNDOM (50); the flexibility of SRP54 is indicated by a black arrow.
Figure 4.
Fig. 4. Structure of the proposed signal peptide binding site. (A) Closed conformation of the hydrophobic groove in the S. solfataricus SRP54/RNA complex. The finger loop is folded into the groove. Helix ML is not shown for clarity. Elements involved in signal peptide binding are named. (B) Superposition of the M domain of S. solfataricus (red) and T. aquaticus (blue) to visualize the different conformations of the signal peptide binding groove including the finger loop and helix M1b. Movements between structures are indicated by black arrows. The position of the conserved motifs GP (green) and PG (pink) differ significantly, the two "anchor" points (Leu-329 and Ile-374) are marked as spheres. (C) Structure of the M domain of T. aquaticus Ffh with the finger loop in an open conformation. A putative signal peptide (gray cylinder) is modeled into the binding site. (D) Model for the conformational changes in the SRP core. SRP54 is shown in a ribbon diagram; color code is as in Fig. 1 A. Rearrangements in SRP54 upon interaction with a signal peptide at the ribosome (see text) are indicated by arrows, the linker region LGMGD is indicated by a blue sphere, the anchor points Leu-329 and the N terminus of helix M2 (Ile-374) as well as the GP and PG motifs are shown as pink spheres. The M[N] domain is adjusted at the four pink spheres to adopt a conformation competent for signal peptide binding as shown in C. The GTP (space-filling model) and the signal peptide (gray cylinder) are placed in their respective binding sites.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21291501 I.Saraogi, and S.O.Shan (2011).
Molecular mechanism of co-translational protein targeting by the signal recognition particle.
  Traffic, 12, 535-542.  
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
  20672053 C.Zwieb, and S.Bhuiyan (2010).
Archaea signal recognition particle shows the way.
  Archaea, 2010, 485051.  
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
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.  
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.  
19219012 E.Schleiff, and R.Tampé (2009).
Membrane proteins take center stage in Frankfurt.
  Nat Chem Biol, 5, 135-139.  
19948960 G.Bozkurt, G.Stjepanovic, F.Vilardi, S.Amlacher, K.Wild, G.Bange, V.Favaloro, K.Rippe, E.Hurt, B.Dobberstein, and I.Sinning (2009).
Structural insights into tail-anchored protein binding and membrane insertion by Get3.
  Proc Natl Acad Sci U S A, 106, 21131-21136.
PDB codes: 3iqw 3iqx
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.  
19219017 I.Sinning, K.Wild, and G.Bange (2009).
Signal sequences get active.
  Nat Chem Biol, 5, 146-147.  
19558326 P.Grudnik, G.Bange, and I.Sinning (2009).
Protein targeting by the signal recognition particle.
  Biol Chem, 390, 775-782.  
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.  
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.  
18400172 M.Selmer, and A.Liljas (2008).
Exit biology: battle for the nascent chain.
  Structure, 16, 498-500.  
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
18618268 U.Ilangovan, S.H.Bhuiyan, C.S.Hinck, J.T.Hoyle, O.N.Pakhomova, C.Zwieb, and A.P.Hinck (2008).
A. fulgidus SRP54 M-domain.
  J Biomol NMR, 41, 241-248.
PDB code: 2jqe
17164479 F.Y.Siu, R.J.Spanggord, and J.A.Doudna (2007).
SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting.
  RNA, 13, 240-250.  
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.  
17186523 J.Gawronski-Salerno, J.S.Coon, P.J.Focia, and D.M.Freymann (2007).
X-ray structure of the T. aquaticus FtsY:GDP complex suggests functional roles for the C-terminal helix of the SRP GTPases.
  Proteins, 66, 984-995.
PDB code: 2iyl
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.  
17576673 S.Berkner, D.Grogan, S.V.Albers, and G.Lipps (2007).
Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-)archaea.
  Nucleic Acids Res, 35, e88.  
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
17086205 C.Schaffitzel, M.Oswald, I.Berger, T.Ishikawa, J.P.Abrahams, H.K.Koerten, R.I.Koning, and N.Ban (2006).
Structure of the E. coli signal recognition particle bound to a translating ribosome.
  Nature, 444, 503-506.
PDB code: 2iy3
16987964 I.L.Mainprize, D.R.Beniac, E.Falkovskaia, R.M.Cleverley, L.M.Gierasch, F.P.Ottensmeyer, and D.W.Andrews (2006).
The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.
  Mol Biol Cell, 17, 5063-5074.  
16469117 K.Römisch, F.W.Miller, B.Dobberstein, and S.High (2006).
Human autoantibodies against the 54 kDa protein of the signal recognition particle block function at multiple stages.
  Arthritis Res Ther, 8, R39.  
17086193 M.Halic, M.Blau, T.Becker, T.Mielke, M.R.Pool, K.Wild, I.Sinning, and R.Beckmann (2006).
Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
  Nature, 444, 507-511.
PDB codes: 2j28 2j37
15923378 I.Buskiewicz, A.Kubarenko, F.Peske, M.V.Rodnina, and W.Wintermeyer (2005).
Domain rearrangement of SRP protein Ffh upon binding 4.5S RNA and the SRP receptor FtsY.
  RNA, 11, 947-957.  
16153172 J.Luirink, G.von Heijne, E.Houben, and J.W.de Gier (2005).
Biogenesis of inner membrane proteins in Escherichia coli.
  Annu Rev Microbiol, 59, 329-355.  
16257258 M.Pohlschröder, M.I.Giménez, and K.F.Jarrell (2005).
Protein transport in Archaea: Sec and twin arginine translocation pathways.
  Curr Opin Microbiol, 8, 713-719.  
16299512 R.J.Spanggord, F.Siu, A.Ke, and J.A.Doudna (2005).
RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle.
  Nat Struct Mol Biol, 12, 1116-1122.  
16199578 R.Matsumi, H.Atomi, and T.Imanaka (2005).
Biochemical properties of a putative signal peptide peptidase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  J Bacteriol, 187, 7072-7080.  
16043501 S.Q.Gu, J.Jöckel, P.Beinker, J.Warnecke, Y.P.Semenkov, M.V.Rodnina, and W.Wintermeyer (2005).
Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit.
  RNA, 11, 1374-1384.  
14749771 E.C.Mandon, and R.Gilmore (2004).
GTPase twins in the SRP family.
  Nat Struct Mol Biol, 11, 115-116.  
15546976 F.Chu, S.O.Shan, D.T.Moustakas, F.Alber, P.F.Egea, R.M.Stroud, P.Walter, and A.L.Burlingame (2004).
Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry.
  Proc Natl Acad Sci U S A, 101, 16454-16459.  
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.  
15523481 K.Wild, M.Halic, I.Sinning, and R.Beckmann (2004).
SRP meets the ribosome.
  Nat Struct Mol Biol, 11, 1049-1053.  
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
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.