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 present ...

    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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Entity ID: 4
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Cell division protein FtsQ AZ98Escherichia coli O157:H7Mutation(s): 0 
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Apolipoprotein A-I A0, A1200Homo sapiensMutation(s): 0 
Gene Names: APOA1
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GTEx:  ENSG00000118137
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Entity ID: 6
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30S ribosomal protein S2 AB240Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsB, b0169, JW0164
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30S ribosomal protein S3 AC232Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsC, b3314, JW3276
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30S ribosomal protein S4 AD205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
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Entity ID: 9
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30S ribosomal protein S5 AE166Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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30S ribosomal protein S6 AF135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsF, b4200, JW4158
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30S ribosomal protein S7 AG178Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsG, b3341, JW3303
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30S ribosomal protein S8 AH129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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30S ribosomal protein S9 AI129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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30S ribosomal protein S10 AJ103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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30S ribosomal protein S11 AK128Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsK, b3297, JW3259
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30S ribosomal protein S12 AL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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30S ribosomal protein S13 AM117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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30S ribosomal protein S14 AN100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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30S ribosomal protein S15 AO88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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30S ribosomal protein S16 AP82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsP, b2609, JW2590
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30S ribosomal protein S17 AQ83Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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30S ribosomal protein S18 AR74Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsR, b4202, JW4160
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30S ribosomal protein S19 AS91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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30S ribosomal protein S20 AT86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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30S ribosomal protein S21 AU70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsU, b3065, JW3037
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Preprotein translocase secY subunit BA435Escherichia coli 536Mutation(s): 0 
Gene Names: secY, ECP_3388
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Preprotein translocase secE subunit BB116Escherichia coli 536Mutation(s): 0 
Gene Names: secE, ECP_4194
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50S ribosomal protein L1 B5234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplA, b3984, JW3947
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50S ribosomal protein L2 B6272Escherichia coli K-12Mutation(s): 0 
Gene Names: rplB, b3317, JW3279
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50S ribosomal protein L3 BD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplC, b3320, JW3282
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50S ribosomal protein L4 BE201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplD, eryA, b3319, JW3281
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50S ribosomal protein L5 BF178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplE, b3308, JW3270
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50S ribosomal protein L6 BG176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplF, b3305, JW3267
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50S ribosomal protein L9 BH149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplI, b4203, JW4161
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50S ribosomal protein L11 BI141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplK, relC, b3983, JW3946
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50S ribosomal protein L13 BJ142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplM, b3231, JW3200
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50S ribosomal protein L14 BK123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplN, b3310, JW3272
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50S ribosomal protein L15 BL144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplO, b3301, JW3263
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50S ribosomal protein L16 BM136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplP, b3313, JW3275
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50S ribosomal protein L17 BN127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQ, b3294, JW3256
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50S ribosomal protein L18 BO117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplR, b3304, JW3266
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50S ribosomal protein L19 BP114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplS, b2606, JW2587
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50S ribosomal protein L20 BQ117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplT, pdzA, b1716, JW1706
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50S ribosomal protein L21 BR103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplU, b3186, JW3153
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50S ribosomal protein L22 BS110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplV, eryB, b3315, JW3277
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50S ribosomal protein L23 BT100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplW, b3318, JW3280
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50S ribosomal protein L24 BU103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplX, b3309, JW3271
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50S ribosomal protein L25 BV94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplY, b2185, JW2173
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50S ribosomal protein L27 BW84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmA, b3185, JW3152
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50S ribosomal protein L28 BX77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmB, b3637, JW3612
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50S ribosomal protein L29 BY63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmC, b3312, JW3274
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50S ribosomal protein L30 BZ58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmD, b3302, JW3264
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50S ribosomal protein L32 B056Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmF, b1089, JW1075
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Entity ID: 56
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50S ribosomal protein L33 B154Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmG, b3636, JW3611
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50S ribosomal protein L34 B246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmH, rimA, ssaF, b3703, JW3680
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Entity ID: 58
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50S ribosomal protein L35 B364Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmI, b1717, JW1707
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50S ribosomal protein L36 B438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJ, b3299, JW3261
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MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAAA1542Escherichia coli
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    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    mRNAAX11Escherichia coli
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    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    FtsQ nascent chainAV77Escherichia coli DH1
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    (by identity cutoff)  |  Structure
    Entity ID: 26
    MoleculeChainsLengthOrganismImage
    5S RIBOSOMAL RNAB7120Escherichia coli DH1
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    Entity ID: 27
    MoleculeChainsLengthOrganismImage
    23S RIBOSOMAL RNAB82904Escherichia coli DH1
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PGV
    Query on PGV
    Download Ideal Coordinates CCD File 
    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 Ideal Coordinates 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


    View more in-depth experimental data

    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