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PDBsum entry 2wwb

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
2wwb
Jmol PyMol
Contents
Protein chains
476 a.a. *
68 a.a. *
36 a.a. *
269 a.a. *
153 a.a. *
53 a.a. *
83 a.a. *
127 a.a. *
84 a.a. *
69 a.a. *
37 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
2wwb
Name: Ribosome
Title: Cryo-em structure of the mammalian sec61 complex bound to th actively translating wheat germ 80s ribosome
Structure: Protein transport protein sec61 subunit alpha iso chain: a. Synonym: sec61alpha, sec61 alpha-1. Protein transport protein sec61 subunit gamma. Chain: b. Synonym: sec61gamma. Protein transport protein sec61 subunit beta. Chain: c. Synonym: sec61beta.
Source: Canis lupus familiaris. Dog. Organism_taxid: 9615. Organ: pancreas. Triticum aestivum. Bread wheat. Organism_taxid: 4565. Other_details: coordinate source originally from saccharomy cerevisiae.
Authors: T.Becker,E.Mandon,S.Bhushan,A.Jarasch,J.P.Armache,S.Funes,F. J.Gumbart,T.Mielke,O.Berninghausen,K.Schulten,E.Westhof,R.G R.Beckmann
Key ref:
T.Becker et al. (2009). Structure of monomeric yeast and Mammalian sec61 complexes interacting with the translating ribosome. Science, 326, 1369-1373. PubMed id: 19933108 DOI: 10.1126/science.1178535
Date:
22-Oct-09     Release date:   08-Dec-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P38377  (S61A1_CANFA) -  Protein transport protein Sec61 subunit alpha isoform 1
Seq:
Struc:
476 a.a.
476 a.a.
Protein chain
Pfam   ArchSchema ?
P60058  (SC61G_CANFA) -  Protein transport protein Sec61 subunit gamma
Seq:
Struc:
68 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
P60467  (SC61B_CANFA) -  Protein transport protein Sec61 subunit beta
Seq:
Struc:
96 a.a.
36 a.a.
Protein chain
Pfam   ArchSchema ?
P49626  (RL4B_YEAST) -  60S ribosomal protein L4-B
Seq:
Struc:
362 a.a.
269 a.a.
Protein chain
Pfam   ArchSchema ?
P05740  (RL17A_YEAST) -  60S ribosomal protein L17-A
Seq:
Struc:
184 a.a.
153 a.a.
Protein chain
No UniProt id for this chain
Struc: 53 a.a.
Protein chain
Pfam   ArchSchema ?
P04456  (RL25_YEAST) -  60S ribosomal protein L25
Seq:
Struc:
142 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P05743  (RL26A_YEAST) -  60S ribosomal protein L26-A
Seq:
Struc:
127 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0C2H8  (RL31A_YEAST) -  60S ribosomal protein L31-A
Seq:
Struc:
113 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX84  (RL35A_YEAST) -  60S ribosomal protein L35-A
Seq:
Struc:
120 a.a.
69 a.a.
Protein chain
Pfam   ArchSchema ?
P04650  (RL39_YEAST) -  60S ribosomal protein L39
Seq:
Struc:
51 a.a.
37 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   15 terms 
  Biological process     pronephric nephron development   21 terms 
  Biochemical function     protein binding     11 terms  

 

 
DOI no: 10.1126/science.1178535 Science 326:1369-1373 (2009)
PubMed id: 19933108  
 
 
Structure of monomeric yeast and Mammalian sec61 complexes interacting with the translating ribosome.
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, R.Beckmann.
 
  ABSTRACT  
 
The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may serve as an active PCC. We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. In combination with biochemical data, we found that in both idle and active states, the Sec complex is not oligomeric and interacts mainly via two cytoplasmic loops with the universal ribosomal adaptor site. In the active state, the ribosomal tunnel and a central pore of the monomeric PCC were occupied by the nascent chain, contacting loop 6 of the Sec complex. This provides a structural basis for the activity of a solitary Sec complex in cotranslational protein translocation.
 
  Selected figure(s)  
 
Figure 1.
View larger version (72K): [in this window] [in a new window] Fig. 1. Cryo-EM reconstructions of 80S ribosome-Ssh1 complexes. Cryo-EM reconstructions of the idle (A) and active (B) 80S-Ssh1 complex at 9 Å resolution. (C) Map of the 80S ribosome with ES27 in the exit conformation at 8 Å. Color code: 40S subunit, yellow; 60S subunit, blue; P-site tRNA/nascent polypeptide chain, green; Ssh1 complexes (PCC), red. NC, nascent chain.
Figure 6.
View larger version (64K): [in this window] [in a new window] Fig. 6. Conformation and nascent polypeptide chain interactions of the RNC-bound mammalian Sec61 complex. (A) Fit of the Sec61 model (red ribbons) into the density (gray transparent mesh). Side views on the lateral gate (top) and cytosolic loops L6 and L8 (bottom). (B) Crystal structure of the M. jannaschii SecYEβ complex (gray) (13) superimposed on an Sec61 model. The C- and N-terminal halves are shown in red and dark blue, transmembrane (TM) helix 7 in yellow, and TM helix 2 in light blue. β (dark red) and subunits (SecE, magenta) are indicated. (C) Side view [top, as in (A)] and top view [bottom, as in (B)] of the Sec61 model and extra density for the nascent polypeptide chain (green). (D) Side view as in top panel of (C), but rotated to focus on the nascent chain (green). Color code as in Fig. 2E. (E) Schematic representation of an actively translating and translocating eukaryotic ribosome-Sec61 complex with a single copy acting as PCC.
 
  The above figures are reprinted by permission from the AAAs: Science (2009, 326, 1369-1373) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23202586 C.Leidig, G.Bange, J.Kopp, S.Amlacher, A.Aravind, S.Wickles, G.Witte, E.Hurt, R.Beckmann, and I.Sinning (2013).
Structural characterization of a eukaryotic chaperone-the ribosome-associated complex.
  Nat Struct Mol Biol, 20, 23-28.
PDB codes: 4gmq 4gni
23142978 B.Bradatsch, C.Leidig, S.Granneman, M.Gnädig, D.Tollervey, B.Böttcher, R.Beckmann, and E.Hurt (2012).
Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel.
  Nat Struct Mol Biol, 19, 1234-1241.
PDB code: 3j2i
23142985 B.J.Greber, D.Boehringer, C.Montellese, and N.Ban (2012).
Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit.
  Nat Struct Mol Biol, 19, 1228-1233.
PDB codes: 4b6a 4b6b
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.  
22358840 T.Becker, S.Franckenberg, S.Wickles, C.J.Shoemaker, A.M.Anger, J.P.Armache, H.Sieber, C.Ungewickell, O.Berninghausen, I.Daberkow, A.Karcher, M.Thomm, K.P.Hopfner, R.Green, and R.Beckmann (2012).
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
  Nature, 482, 501-506.
PDB codes: 3j15 3j16
22864288 Y.Mao, L.Wang, C.Gu, A.Herschhorn, S.H.Xiang, H.Haim, X.Yang, and J.Sodroski (2012).
Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.
  Nat Struct Mol Biol, 19, 893-899.  
21419343 A.Khushoo, Z.Yang, A.E.Johnson, and W.R.Skach (2011).
Ligand-driven vectorial folding of ribosome-bound human CFTR NBD1.
  Mol Cell, 41, 682-692.  
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.  
21562565 E.Park, and T.A.Rapoport (2011).
Preserving the membrane barrier for small molecules during bacterial protein translocation.
  Nature, 473, 239-242.  
21518907 F.Bonardi, E.Halza, M.Walko, F.Du Plessis, N.Nouwen, B.L.Feringa, and A.J.Driessen (2011).
Probing the SecYEG translocation pore size with preproteins conjugated with sizable rigid spherical molecules.
  Proc Natl Acad Sci U S A, 108, 7775-7780.  
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.  
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
21317362 J.Gumbart, C.Chipot, and K.Schulten (2011).
Free-energy cost for translocon-assisted insertion of membrane proteins.
  Proc Natl Acad Sci U S A, 108, 3596-3601.  
21205638 J.Rabl, M.Leibundgut, S.F.Ataide, A.Haag, and N.Ban (2011).
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
  Science, 331, 730-736.
PDB codes: 2xzm 2xzn
21056980 K.Deville, V.A.Gold, A.Robson, S.Whitehouse, R.B.Sessions, S.A.Baldwin, S.E.Radford, and I.Collinson (2011).
The oligomeric state and arrangement of the active bacterial translocon.
  J Biol Chem, 286, 4659-4669.  
21487438 K.S.Matlin (2011).
Spatial expression of the genome: the signal hypothesis at forty.
  Nat Rev Mol Cell Biol, 12, 333-340.  
  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.  
22086371 R.S.Hegde, and R.J.Keenan (2011).
Tail-anchored membrane protein insertion into the endoplasmic reticulum.
  Nat Rev Mol Cell Biol, 12, 787-798.  
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.  
21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
20534348 A.L.Starosta, V.V.Karpenko, A.V.Shishkina, A.Mikolajka, N.V.Sumbatyan, F.Schluenzen, G.A.Korshunova, A.A.Bogdanov, and D.N.Wilson (2010).
Interplay between the ribosomal tunnel, nascent chain, and macrolides influences drug inhibition.
  Chem Biol, 17, 504-514.  
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.  
20203009 B.Zhang, and T.F.Miller (2010).
Hydrophobically stabilized open state for the lateral gate of the Sec translocon.
  Proc Natl Acad Sci U S A, 107, 5399-5404.  
20576878 C.G.Tate (2010).
Biochemistry. Membrane protein gymnastics.
  Science, 328, 1644-1645.  
20562414 F.Jossinet, T.E.Ludwig, and E.Westhof (2010).
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.
  Bioinformatics, 26, 2057-2059.  
20183845 J.Hsin, D.E.Chandler, J.Gumbart, C.B.Harrison, M.Sener, J.Strumpfer, and K.Schulten (2010).
Self-assembly of photosynthetic membranes.
  Chemphyschem, 11, 1154-1159.  
20974910 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
  Proc Natl Acad Sci U S A, 107, 19754-19759.
PDB codes: 3iz5 3iz6 3iz7 3iz9 3izr
20980660 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 107, 19748-19753.
PDB code: 3izd
20117091 K.Ito, S.Chiba, and K.Pogliano (2010).
Divergent stalling sequences sense and control cellular physiology.
  Biochem Biophys Res Commun, 393, 1-5.  
20462496 L.G.Trabuco, C.B.Harrison, E.Schreiner, and K.Schulten (2010).
Recognition of the regulatory nascent chain TnaC by the ribosome.
  Structure, 18, 627-637.  
20392820 R.Babiano, and J.de la Cruz (2010).
Ribosomal protein L35 is required for 27SB pre-rRNA processing in Saccharomyces cerevisiae.
  Nucleic Acids Res, 38, 5177-5192.  
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
20932481 S.Bhushan, H.Meyer, A.L.Starosta, T.Becker, T.Mielke, O.Berninghausen, M.Sattler, D.N.Wilson, and R.Beckmann (2010).
Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide.
  Mol Cell, 40, 138-146.
PDB code: 2xl1
21124925 S.L.Hutson, E.Mui, K.Kinsley, W.H.Witola, M.S.Behnke, K.El Bissati, S.P.Muench, B.Rohrman, S.R.Liu, R.Wollmann, Y.Ogata, A.Sarkeshik, J.R.Yates, and R.McLeod (2010).
T. gondii RP promoters & knockdown reveal molecular pathways associated with proliferation and cell-cycle arrest.
  PLoS One, 5, e14057.  
20156192 Z.Cheng (2010).
Protein translocation through the Sec61/SecY channel.
  Biosci Rep, 30, 201-207.  
19933110 B.Seidelt, C.A.Innis, D.N.Wilson, M.Gartmann, J.P.Armache, E.Villa, L.G.Trabuco, T.Becker, T.Mielke, K.Schulten, T.A.Steitz, and R.Beckmann (2009).
Structural insight into nascent polypeptide chain-mediated translational stalling.
  Science, 326, 1412-1415.
PDB codes: 2wwl 2wwq
19965743 M.Kampmann, and G.Blobel (2009).
Nascent proteins caught in the act.
  Science, 326, 1352-1353.  
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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