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 endoplasmic reticulum where it can bind to translating ribosomes for co-translational protein transport ...

    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 S24ED [auth BY]138Triticum aestivumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8EE [auth BI]220Triticum aestivumMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10EF [auth BK]183Triticum aestivumMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12EG [auth BM]171Triticum aestivumMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S31eH [auth Bf]155Triticum aestivumMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12I [auth BX]142Triticum aestivumMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1J [auth Bg]380Triticum aestivumMutation(s): 0 
Gene Names: TaGB1
Find proteins for Q8LNY6 (Triticum aestivum)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3K [auth BD]208Triticum aestivumMutation(s): 0 
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Entity ID: 12
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40S ribosomal protein S4EL [auth BE]265Triticum aestivumMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7M [auth BF]191Triticum aestivumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9N [auth BQ]149Triticum aestivumMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10O [auth BU]128Triticum aestivumMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11P [auth BO]151Triticum aestivumMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13Q [auth BS]152Triticum aestivumMutation(s): 0 
Find proteins for Q8L806 (Triticum aestivum)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15R [auth BN]151Triticum aestivumMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17S [auth BL]160Triticum aestivumMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19ET [auth BT]146Triticum aestivumMutation(s): 0 
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Entity ID: 21
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40S ribosomal protein S19U [auth BP]154Triticum aestivumMutation(s): 0 
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Entity ID: 22
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40S ribosomal protein S25EV [auth BZ]108Triticum aestivumMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28EW [auth Bc]65Triticum aestivumMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8X [auth BW]130Triticum aestivumMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14Y [auth Bd]56Triticum aestivumMutation(s): 0 
Gene Names: RPS29
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27EZ [auth Bb]86Triticum aestivumMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30EAA [auth Be]62Triticum 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
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17ECA [auth BR]141Triticum aestivumMutation(s): 0 
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Entity ID: 30
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40S ribosomal protein S1EDA [auth BB]262Triticum aestivumMutation(s): 0 
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Entity ID: 31
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40S ribosomal protein S21EEA [auth BV]82Triticum aestivumMutation(s): 0 
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Entity ID: 32
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40S ribosomal protein S26EFA [auth Ba]133Triticum aestivumMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4GA [auth BJ]195Triticum aestivumMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5HA [auth BC]263Triticum aestivumMutation(s): 0 
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Entity ID: 35
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40S ribosomal protein S6IA [auth BG]245Triticum aestivumMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7EJA [auth BH]189Triticum aestivumMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8EKA [auth CG]257Triticum aestivumMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21ELA [auth CT]164Triticum aestivumMutation(s): 0 
Gene Names: RPL21
Find proteins for F4YWL9 (Triticum aestivum)
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Entity ID: 39
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60S ribosomal protein L27EMA [auth CZ]136Triticum aestivumMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L1NA [auth Cz]216Triticum aestivumMutation(s): 0 
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Entity ID: 41
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60S ribosomal protein L2OA [auth CA]261Triticum aestivumMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5PA [auth CJ]180Triticum aestivumMutation(s): 0 
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Entity ID: 43
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60S ribosomal protein L6QA [auth CH]190Triticum aestivumMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14RA [auth CV]140Triticum aestivumMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15ESA [auth CN]200Triticum aestivumMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15TA [auth Ca]144Triticum aestivumMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18EUA [auth CQ]188Triticum aestivumMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18VA [auth CD]304Triticum aestivumMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19EWA [auth CR]209Triticum aestivumMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22XA [auth CP]171Triticum aestivumMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23YA [auth CX]152Triticum aestivumMutation(s): 0 
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Entity ID: 52
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60S ribosomal protein L24EZA [auth CW]162Triticum aestivumMutation(s): 0 
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Entity ID: 53
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60S ribosomal protein L24AB [auth CY]150Triticum aestivumMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein L28EBB [auth Cr]147Triticum aestivumMutation(s): 0 
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Entity ID: 55
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60S ribosomal protein L30ECB [auth Cc]112Triticum aestivumMutation(s): 0 
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Entity ID: 56
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60S ribosomal protein L31EDB [auth Cd]123Triticum aestivumMutation(s): 0 
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Entity ID: 57
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60S ribosomal protein L32EEB [auth Ce]133Triticum aestivumMutation(s): 0 
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Entity ID: 58
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60S ribosomal protein L37EFB [auth Cj]94Triticum aestivumMutation(s): 0 
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Entity ID: 59
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60S ribosomal protein L39EGB [auth Cl]51Triticum aestivumMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L44EHB [auth Co]105Triticum aestivumMutation(s): 0 
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Entity ID: 61
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60S ribosomal protein L14EIB [auth CM]134Triticum aestivumMutation(s): 0 
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Entity ID: 62
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60S ribosomal protein L20JB [auth CS]178Triticum aestivumMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L22EKB [auth CU]130Triticum aestivumMutation(s): 0 
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Entity ID: 64
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60S ribosomal protein L36ELB [auth Ci]112Triticum aestivumMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L11MB [auth CK]166Triticum aestivumMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein P1NB [auth Cu], OB [auth Cv]110Triticum aestivumMutation(s): 0 
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Entity ID: 67
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Acidic ribosomal protein P2PB [auth Cs], QB [auth Ct]113Triticum aestivumMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29RB [auth Ch]124Triticum aestivumMutation(s): 0 
Gene Names: RPL35
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Entity ID: 69
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60S ribosomal protein L30SB [auth CF]244Triticum aestivumMutation(s): 0 
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Entity ID: 70
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60S acidic ribosomal protein P0TB [auth Cq]319Triticum aestivumMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3UB [auth CB]389Triticum 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 L4VB [auth CC]405Triticum aestivumMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13WB [auth CO]206Triticum aestivumMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L43EXB [auth Cp]92Triticum aestivumMutation(s): 0 
Gene Names: TAA_ctg0616b.00240.1TRAES_3BF073800030CFD_c1
Find proteins for D8L9P6 (Triticum aestivum)
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Entity ID: 75
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60S ribosomal protein L16YB [auth CI]224Triticum aestivumMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L41EZB [auth Cn]25Triticum aestivumMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L40EAC [auth Cm]53Triticum aestivumMutation(s): 0 
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Entity ID: 78
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60S ribosomal protein L13EBC [auth CL]208Triticum aestivumMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L6ECC [auth CE]219Triticum aestivumMutation(s): 0 
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Entity ID: 80
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60S ribosomal protein L33EDC [auth Cf]111Triticum aestivumMutation(s): 0 
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Entity ID: 81
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60S ribosomal protein L38EEC [auth Ck]69Triticum aestivumMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29EFC [auth Cb]60Triticum aestivumMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34EGC [auth Cg]119Triticum aestivumMutation(s): 0 
Find proteins for Q5I7K8 (Triticum aestivum)
Explore Q5I7K8 
Go to UniProtKB:  Q5I7K8
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth Ad]1810Triticum aestivum
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Entity ID: 2
MoleculeChainsLengthOrganismImage
P-site tRNAB [auth Ae]75Triticum aestivum
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'C [auth Af]11Triticum aestivum
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    Entity ID: 84
    MoleculeChainsLengthOrganismImage
    60S ribosomal RNAHC [auth Aa]3391Triticum aestivum
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    Entity ID: 85
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNAIC [auth Ac]160Triticum aestivum
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    Entity ID: 86
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAJC [auth Ab]120Triticum aestivum
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    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  (Full details and data files)

    • 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