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PDBsum entry 3dkn

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protein dna_rna Protein-protein interface(s) links
Protein transport/RNA PDB id
3dkn
Jmol
Contents
Protein chains
430 a.a. *
65 a.a. *
32 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
3dkn
Name: Protein transport/RNA
Title: Sec61 in the canine ribosome-channel complex from the endoplasmic reticulum
Structure: Preprotein translocase subunit secy. Chain: a. Synonym: protein transport protein sec61 subunit alpha homolog. Preprotein translocase subunit sece. Chain: b. Synonym: protein transport protein sec61 gamma subunit homolog. Preprotein translocase subunit secg.
Source: Canis lupus familiaris. Organism_taxid: 9615. Organism_taxid: 9615
Authors: J.-F.Menetret,C.Akey
Key ref:
J.F.Ménétret et al. (2008). Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Structure, 16, 1126-1137. PubMed id: 18611385 DOI: 10.1016/j.str.2008.05.003
Date:
25-Jun-08     Release date:   19-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q60175  (SECY_METJA) -  Protein translocase subunit SecY
Seq:
Struc:
436 a.a.
430 a.a.
Protein chain
Pfam   ArchSchema ?
Q57817  (SECE_METJA) -  Protein translocase subunit SecE
Seq:
Struc:
74 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P60460  (SECG_METJA) -  Preprotein translocase subunit SecG
Seq:
Struc:
53 a.a.
32 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     transport   4 terms 
  Biochemical function     P-P-bond-hydrolysis-driven protein transmembrane transporter activity     1 term  

 

 
DOI no: 10.1016/j.str.2008.05.003 Structure 16:1126-1137 (2008)
PubMed id: 18611385  
 
 
Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.
J.F.Ménétret, R.S.Hegde, M.Aguiar, S.P.Gygi, E.Park, T.A.Rapoport, C.W.Akey.
 
  ABSTRACT  
 
During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from mammalian endoplasmic reticulum in which the channel has been visualized at 11 A resolution. In this complex, single copies of Sec61 and TRAP associate with a nontranslating ribosome and this stoichiometry was verified by quantitative mass spectrometry. A bilayer-like density surrounds the channel and can be attributed to lipid and detergent. The crystal structure of an archaeal homolog of the Sec61 complex was then docked into the map. In this model, two cytoplasmic loops of Sec61 may interact with RNA helices H6, H7, and H50, while the central pore is located below the ribosome tunnel exit. Hence, this copy of Sec61 is positioned to capture and translocate the nascent chain. Finally, we show that mammalian and bacterial ribosome-channel complexes have similar architectures.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The 6/7 and 8/9 Loops of Sec61 Form the Major Connection with the Ribosome
(A) An oblique front view of the RCC is shown. The RCC is color coded as described in Figure 1A. The small (S) and large (L) subunits are labeled. A single major connection spans the gap between the ribosome and the channel.
(B) A close-up is shown of the junction between the ribosome and the membrane-like disk. The positions of connections observed in previous maps at a lower threshold (C1, C2, and C4) are indicated. Also shown are the regions of TRAP (stalk, lumenal domain [LD]).
(C) A thin slab containing the interface between the ribosome and the channel is shown. Helices 50 and 7 in the large subunit interact with the loops of Sec61α near the tunnel exit (T). Density for the connection is shown as a transparent surface overlayed on the modeled loops (shown as ribbons).
(D) A bottom view shows the insertion of the 6/7 and 8/9 loops into a pocket at the exit tunnel. The loop density is shown in magenta and the large subunit is shown in blue. The tunnel is marked with a dot and a line that points into the large subunit, toward the small subunit (yellow surface).
(E) This view is similar to (D) but the surface of the large subunit is semitransparent to show the atomic model of the ribosome (2KZR) in this region.
(F) The 6/7 and 8/9 loops are shown within a binding pocket which is formed by H6, H7, and H50, along with proteins L23ae, L35e, and L39e. Basic residues in the Sec61 loops are shown in yellow and are labeled in the inset on the right.
(G) A rotated view of (F) is shown. A small helix of L39e is close to the 8/9 loop, and L35e helps to form the back of the binding pocket.
Figure 3.
Figure 3. Docking the Sec61 Complex into the Electron Density Map
(A) A bottom view is shown of the RCC with the membrane-embedded region rendered semitransparent to show the docked SecY model.
(B) A low-density Y-shaped region is present within the membrane-like disk and nearly encircles the embedded region of Sec61. The Y-like region is indicated by a dashed line. The electron density map was truncated to 17 Å resolution for (B) and (C). The Sec61 complex was modeled with a crystal structure of SecY and is color coded as follows. The N-terminal half of SecY/Sec61α is colored in red, while the C-terminal half is shown in blue. The SecE/γ subunit is shown in green and the Secβ subunit is shown in tan.
(C) The docked SecY in the channel region is viewed from the ribosome.
(D) A ribbon model of the SecY complex is shown and the helices are numbered. This view is from the ribosome and is similar to that in (E) and (F). The surface helix of the SecE/Sec61γ is labeled (γ-S helix) and helix 2a is shown in purple.
(E) A cross-section is shown of the Sec61 region from the full 3D map truncated at 11 Å resolution. A thin slab encompasses the lumenal side of the channel and the SecY model fits within a low-density feature (marked with dashed line). Helices of the docked model are numbered (van den Berg et al., 2004).
(F) A thicker slab is shown which contains the entire membrane-embedded region of Sec61.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1126-1137) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21562565 E.Park, and T.A.Rapoport (2011).
Preserving the membrane barrier for small molecules during bacterial protein translocation.
  Nature, 473, 239-242.  
21102557 F.Erdmann, N.Schäuble, S.Lang, M.Jung, A.Honigmann, M.Ahmad, J.Dudek, J.Benedix, A.Harsman, A.Kopp, V.Helms, A.Cavalié, R.Wagner, and R.Zimmermann (2011).
Interaction of calmodulin with Sec61α limits Ca2+ leakage from the endoplasmic reticulum.
  EMBO J, 30, 17-31.  
21161320 H.Ishikawa, and G.N.Barber (2011).
The STING pathway and regulation of innate immune signaling in response to DNA pathogens.
  Cell Mol Life Sci, 68, 1157-1165.  
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
  21255212 P.Kuhn, B.Weiche, L.Sturm, E.Sommer, F.Drepper, B.Warscheid, V.Sourjik, and H.G.Koch (2011).
The bacterial SRP receptor, SecA and the ribosome use overlapping binding sites on the SecY translocon.
  Traffic, 12, 563-578.  
20709746 B.M.Wilkinson, J.K.Brownsword, C.J.Mousley, and C.J.Stirling (2010).
Sss1p is required to complete protein translocon activation.
  J Biol Chem, 285, 32671-32677.  
20797628 F.Brandt, L.A.Carlson, F.U.Hartl, W.Baumeister, and K.Grünewald (2010).
The three-dimensional organization of polyribosomes in intact human cells.
  Mol Cell, 39, 560-569.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20622844 P.Mallick, and B.Kuster (2010).
Proteomics: a pragmatic perspective.
  Nat Biotechnol, 28, 695-709.  
19955210 Y.Kida, C.Kume, M.Hirano, and M.Sakaguchi (2010).
Environmental transition of signal-anchor sequences during membrane insertion via the endoplasmic reticulum translocon.
  Mol Biol Cell, 21, 418-429.  
21111237 Y.Shibata, T.Shemesh, W.A.Prinz, A.F.Palazzo, M.M.Kozlov, and T.A.Rapoport (2010).
Mechanisms determining the morphology of the peripheral ER.
  Cell, 143, 774-788.  
19776740 H.Ishikawa, Z.Ma, and G.N.Barber (2009).
STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity.
  Nature, 461, 788-792.  
19535397 J.A.Hiss, and G.Schneider (2009).
Architecture, function and prediction of long signal peptides.
  Brief Bioinform, 10, 569-578.  
19913480 J.Gumbart, L.G.Trabuco, E.Schreiner, E.Villa, and K.Schulten (2009).
Regulation of the protein-conducting channel by a bound ribosome.
  Structure, 17, 1453-1464.
PDB codes: 3kc4 3kcr
19139097 K.Dalal, N.Nguyen, M.Alami, J.Tan, T.F.Moraes, W.C.Lee, R.Maurus, S.S.Sligar, G.D.Brayer, and F.Duong (2009).
Structure, Binding, and Activity of Syd, a SecY-interacting Protein.
  J Biol Chem, 284, 7897-7902.
PDB code: 3ffv
19933108 T.Becker, S.Bhushan, A.Jarasch, J.P.Armache, S.Funes, F.Jossinet, J.Gumbart, T.Mielke, O.Berninghausen, K.Schulten, E.Westhof, R.Gilmore, E.C.Mandon, and R.Beckmann (2009).
Structure of monomeric yeast and Mammalian sec61 complexes interacting with the translating ribosome.
  Science, 326, 1369-1373.
PDB codes: 2ww9 2wwa 2wwb
19491932 W.R.Skach (2009).
Cellular mechanisms of membrane protein folding.
  Nat Struct Mol Biol, 16, 606-612.  
19857245 X.Zhao, and J.Jäntti (2009).
Functional characterization of the trans-membrane domain interactions of the Sec61 protein translocation complex beta-subunit.
  BMC Cell Biol, 10, 76.  
18671729 T.A.Rapoport (2008).
Protein transport across the endoplasmic reticulum membrane.
  FEBS J, 275, 4471-4478.  
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.