4V7E

Model of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.

Gogala, M.Becker, T.Beatrix, B.Armache, J.P.Barrio-Garcia, C.Berninghausen, O.Beckmann, R.

(2014) Nature 506: 107-110

  • DOI: 10.1038/nature12950
  • Primary Citation of Related Structures:  
    4CG5, 4CG6, 4CG7, 4V7E

  • PubMed Abstract: 
  • The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In eukaryotic cells the PCC is located in the membrane of ...

    The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In eukaryotic cells the PCC is located in the membrane of the endoplasmic reticulum where it can bind to translating ribosomes for co-translational protein transport. The Sec complex consists of three subunits (Sec61α, β and γ) and provides an aqueous environment for the translocation of hydrophilic peptides as well as a lateral opening in the Sec61α subunit that has been proposed to act as a gate for the membrane partitioning of hydrophobic domains. A plug helix and a so-called pore ring are believed to seal the PCC against ion flow and are proposed to rearrange for accommodation of translocating peptides. Several crystal and cryo-electron microscopy structures revealed different conformations of closed and partially open Sec61 and SecY complexes. However, in none of these samples has the translocation state been unambiguously defined biochemically. Here we present cryo-electron microscopy structures of ribosome-bound Sec61 complexes engaged in translocation or membrane insertion of nascent peptides. Our data show that a hydrophilic peptide can translocate through the Sec complex with an essentially closed lateral gate and an only slightly rearranged central channel. Membrane insertion of a hydrophobic domain seems to occur with the Sec complex opening the proposed lateral gate while rearranging the plug to maintain an ion permeability barrier. Taken together, we provide a structural model for the basic activities of the Sec61 complex as a protein-conducting channel.


    Related Citations: 
    • Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
      Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soding, J., Westhof, E., Wilson, D.N., Beckmann, R.
      (2010) Proc Natl Acad Sci U S A 107: 19748
    • Localization of eukaryote-specific ribosomal proteins in a 5.5- angstrom cryo-EM map of the 80S eukaryotic ribosome.
      Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soding, J., Westhof, E., Wilson, D.N., Beckmann, R.
      (2010) Proc Natl Acad Sci U S A 107: 19754

    Organizational Affiliation

    Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24EBY138Triticum aestivumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8EBI220Triticum aestivumMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10EBK183Triticum aestivumMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12EBM171Triticum aestivumMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S31eBf155Triticum aestivumMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12BX142Triticum aestivumMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1Bg380Triticum aestivumMutation(s): 0 
Gene Names: TaGB1
Find proteins for Q8LNY6 (Triticum aestivum)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3BD208Triticum aestivumMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4EBE265Triticum aestivumMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7BF191Triticum aestivumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9BQ149Triticum aestivumMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10BU128Triticum aestivumMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11BO151Triticum aestivumMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13BS152Triticum aestivumMutation(s): 0 
Find proteins for Q8L806 (Triticum aestivum)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15BN151Triticum aestivumMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17BL160Triticum aestivumMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19EBT146Triticum aestivumMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19BP154Triticum aestivumMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25EBZ108Triticum aestivumMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28EBc65Triticum aestivumMutation(s): 0 
Find proteins for Q7X9K4 (Triticum aestivum)
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Entity ID: 24
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40S ribosomal protein S8BW130Triticum aestivumMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14Bd56Triticum aestivumMutation(s): 0 
Gene Names: RPS29
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27EBb86Triticum aestivumMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30EBe62Triticum aestivumMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2BA260Triticum aestivumMutation(s): 0 
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Entity ID: 29
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40S ribosomal protein S17EBR141Triticum aestivumMutation(s): 0 
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Entity ID: 30
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40S ribosomal protein S1EBB262Triticum aestivumMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21EBV82Triticum aestivumMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26EBa133Triticum aestivumMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4BJ195Triticum aestivumMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5BC263Triticum aestivumMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6BG245Triticum aestivumMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7EBH189Triticum aestivumMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8ECG257Triticum aestivumMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21ECT164Triticum aestivumMutation(s): 0 
Gene Names: RPL21
Find proteins for F4YWL9 (Triticum aestivum)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27ECZ136Triticum aestivumMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L1Cz216Triticum aestivumMutation(s): 0 
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Entity ID: 41
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60S ribosomal protein L2CA261Triticum aestivumMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5CJ180Triticum aestivumMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6CH190Triticum aestivumMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14CV140Triticum aestivumMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15ECN200Triticum aestivumMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15Ca144Triticum aestivumMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18ECQ188Triticum aestivumMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18CD304Triticum aestivumMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19ECR209Triticum aestivumMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22CP171Triticum aestivumMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23CX152Triticum aestivumMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24ECW162Triticum aestivumMutation(s): 0 
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Entity ID: 53
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60S ribosomal protein L24CY150Triticum aestivumMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein L28ECr147Triticum aestivumMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30ECc112Triticum aestivumMutation(s): 0 
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Entity ID: 56
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60S ribosomal protein L31ECd123Triticum aestivumMutation(s): 0 
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Entity ID: 57
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60S ribosomal protein L32ECe133Triticum aestivumMutation(s): 0 
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Entity ID: 58
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60S ribosomal protein L37ECj94Triticum aestivumMutation(s): 0 
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Entity ID: 59
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60S ribosomal protein L39ECl51Triticum aestivumMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L44ECo105Triticum aestivumMutation(s): 0 
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Entity ID: 61
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60S ribosomal protein L14ECM134Triticum aestivumMutation(s): 0 
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Entity ID: 62
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60S ribosomal protein L20CS178Triticum aestivumMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L22ECU130Triticum aestivumMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36ECi112Triticum aestivumMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L11CK166Triticum aestivumMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein P1CuCv110Triticum aestivumMutation(s): 0 
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Entity ID: 67
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Acidic ribosomal protein P2CsCt113Triticum aestivumMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L29Ch124Triticum aestivumMutation(s): 0 
Gene Names: RPL35
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Entity ID: 69
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60S ribosomal protein L30CF244Triticum aestivumMutation(s): 0 
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Entity ID: 70
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60S acidic ribosomal protein P0Cq319Triticum aestivumMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3CB389Triticum aestivumMutation(s): 0 
Gene Names: RPL3RPL3-A1RPL3A-1
Find proteins for Q7X744 (Triticum aestivum)
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Entity ID: 72
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60S ribosomal protein L4CC405Triticum aestivumMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L13CO206Triticum aestivumMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L43ECp92Triticum aestivumMutation(s): 0 
Gene Names: TAA_ctg0616b.00240.1TRAES_3BF073800030CFD_c1
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Entity ID: 75
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60S ribosomal protein L16CI224Triticum aestivumMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L41ECn25Triticum aestivumMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L40ECm53Triticum aestivumMutation(s): 0 
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Entity ID: 78
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60S ribosomal protein L13ECL208Triticum aestivumMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L6ECE219Triticum aestivumMutation(s): 0 
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Entity ID: 80
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60S ribosomal protein L33ECf111Triticum aestivumMutation(s): 0 
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Entity ID: 81
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60S ribosomal protein L38ECk69Triticum aestivumMutation(s): 0 
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Entity ID: 82
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60S ribosomal protein L29ECb60Triticum aestivumMutation(s): 0 
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Entity ID: 83
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60S ribosomal protein L34ECg119Triticum aestivumMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAAd1810Triticum aestivum
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Entity ID: 2
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P-site tRNAAe75Triticum aestivum
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'Af11Triticum aestivum
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    (by identity cutoff)  |  Structure
    Entity ID: 84
    MoleculeChainsLengthOrganismImage
    60S ribosomal RNAAa3391Triticum aestivum
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    (by identity cutoff)  |  Structure
    Entity ID: 85
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNAAc160Triticum aestivum
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    Entity ID: 86
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAAb120Triticum aestivum
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 5.50 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Revision History 

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other
    • Version 1.2: 2015-04-15
      Changes: Other
    • Version 1.3: 2018-07-18
      Changes: Data collection
    • Version 1.4: 2019-12-18
      Changes: Other