4V6M

Structure of the ribosome-SecYE complex in the membrane environment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.5 of the entry. See complete history


Literature

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.

Frauenfeld, J.Gumbart, J.Sluis, E.O.Funes, S.Gartmann, M.Beatrix, B.Mielke, T.Berninghausen, O.Becker, T.Schulten, K.Beckmann, R.

(2011) Nat Struct Mol Biol 18: 614-621

  • DOI: 10.1038/nsmb.2026
  • Primary Citation of Related Structures:  
    4V6M

  • PubMed Abstract: 
  • The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we pre ...

    The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane.


    Organizational Affiliation

    Gene Center, Department for Biochemistry, University of Munich, Munich, Germany.



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Cell division protein FtsQAZ98Escherichia coli O157:H7Mutation(s): 0 
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Apolipoprotein A-IA0A1200Homo sapiensMutation(s): 0 
Gene Names: APOA1
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30S ribosomal protein S2AB240Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3AC232Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S4AD205Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S5AE166Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S6AF135Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S7AG178Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8AH129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S9AI129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S10AJ103Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11AK128Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S12AL123Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S13AM117Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S14AN100Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S15AO88Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S16AP82Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S17AQ83Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S18AR74Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S19AS91Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S20AT86Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S21AU70Escherichia coli K-12Mutation(s): 0 
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Preprotein translocase secY subunitBA435Escherichia coli 536Mutation(s): 0 
Gene Names: secYECP_3388
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Preprotein translocase secE subunitBB116Escherichia coli 536Mutation(s): 0 
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50S ribosomal protein L1B5234Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L2B6272Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L3BD209Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L4BE201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L5BF178Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6BG176Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L9BH149Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L11BI141Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L13BJ142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14BK123Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L15BL144Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L16BM136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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50S ribosomal protein L17BN127Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18BO117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19BP114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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50S ribosomal protein L20BQ117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21BR103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22BS110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23BT100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24BU103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25BV94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L27BW84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28BX77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29BY63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L30BZ58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32B056Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33B154Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34B246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35B364Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36B438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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16S RIBOSOMAL RNAAA1542Escherichia coli
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    mRNAAX11Escherichia coli
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    FtsQ nascent chainAV77Escherichia coli DH1
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    5S RIBOSOMAL RNAB7120Escherichia coli DH1
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    23S RIBOSOMAL RNAB82904Escherichia coli DH1
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    Ligands 2 Unique
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    PGV
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    A0, A1, AZ, B8, BA, BB
    (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
    C40 H77 O10 P
    ADYWCMPUNIVOEA-GPJPVTGXSA-N
     Ligand Interaction
    PEV
    Query on PEV

    Download CCD File 
    A0, A1, AZ, B8, BA, BB
    (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
    C39 H78 N O8 P
    RPJZYOHZALDGKI-QNGWXLTQSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 7.10 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-08-20
      Changes: Database references, Structure summary
    • Version 1.2: 2014-12-10
      Changes: Other
    • Version 1.3: 2015-04-01
      Changes: Other
    • Version 1.4: 2018-07-18
      Changes: Data collection
    • Version 1.5: 2019-12-18
      Changes: Database references, Other