6S0K

Ribosome nascent chain in complex with SecA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA.

Wang, S.Jomaa, A.Jaskolowski, M.Yang, C.I.Ban, N.Shan, S.O.

(2019) Nat Struct Mol Biol 26: 919-929

  • DOI: 10.1038/s41594-019-0297-8
  • Primary Citation of Related Structures:  
    6S0K

  • PubMed Abstract: 
  • Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane ...

    Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA. sshan@caltech.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 C273Escherichia coliMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L3 D209Escherichia coliMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L4 E201Escherichia coliMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L5 F179Escherichia coliMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L6 G177Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 H149Escherichia coliMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L10 I165Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L11 J142Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L13 K142Escherichia coliMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L14 L123Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L15 M144Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L16 N136Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L17 O127Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L18 P117Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L19 Q115Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L20 R118Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L21 S103Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 T110Escherichia coliMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L23 U100Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L24 V104Escherichia coliMutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L25 W94Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L27 X85Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L28 Y78Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L29 Z63Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 a59Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L32 b57Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L33 c55Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L34 d46Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 e65Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 f38Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecA h838Escherichia coliMutation(s): 0 
Gene Names: 
secAazidivA8C65_16295A9P13_21545AAW05_10535ACN68_30130ACN81_28915ACU57_16035ACU90_26895AM270_12025AUQ13_07855AWB10_21395B9T59_07925BANRA_00479BANRA_00570BANRA_02341BANRA_03271BEN53_02700BK248_21050BK292_13315BK296_02885BMA87_13090BMT91_01720BON63_04275BON71_00565BON86_13400BON98_07385BUE81_03750BvCms2454_01608BvCmsHHP001_03356BvCmsKSP026_04779BvCmsNSNP036_02420BvCmsOUP014_04165BvCmsSINP011_00780BvCmsSIP019_01094BvCmsSIP044_04874BVL39_02565BW690_21995BZL31_13370C5F73_07575C5N07_08195C6669_04640C7235_20610C9098_16455C9Z37_13980C9Z39_04640CA593_03250CDL37_06840CF006_13815CG692_01215CIG45_07370CJU64_00500CO706_22680COD46_06255CQP61_22465CRM83_15470CV83915_01479D0X26_09800D3821_05850D4638_02165D4V08_18855D6T60_04390D6W00_08265D9D44_07130D9E19_08845D9G69_06180D9H94_05480D9J52_04910D9J63_15660D9K48_09625DAH18_05665DAH34_04570DBQ99_21740DEO04_16725DEO20_19340DJ503_00515DK132_00510DL292_03460DL326_07905DLY41_10265DM129_16885DM267_10025DM296_04045DM382_05455DM973_00505DQE91_03605DQF36_06390DT034_05720DTL43_06305DWB25_20700DXT69_01850E0I42_17625E0K84_13195E2114_00090E2115_19590E2119_07760E2127_05565E2128_00995E2129_03210E2134_11625E4A44_06050E4K51_06140E4K55_07315E4K59_00505E4K60_04245E4K61_10540E5P24_14230E5S56_11230EA213_09545EAI52_02055EB476_14445EBA46_02260EC1094V2_3755EC3234A_2c00820EC3426_00849ECTO6_03969ED307_12420EEP23_00520EHH55_17330EI021_04690EI028_09845EI041_03510EIZ93_07545EL75_3664EL79_3774EL80_3721ELT20_04120ELT49_10590ELT58_18630ELV08_09210EPT01_02945ExPECSC038_04062EXX24_10555EXX71_12680EXX78_15220EYD11_18890EYY78_10355F1E13_08205F9059_11930F9Z53_10430FORC82_3946FV293_03245FZ043_03670FZN06_10525G3V64_13545G5603_15580G5608_17025G5616_00540G5688_03895GHR40_00935GII67_17370GII91_19860GJ11_00520GKF39_00845GKF74_00250GKF86_00845GKF89_02140GNZ03_07645GNZ05_10165GP654_11465GP661_02630GP666_05415GP671_09275GP935_09510GP979_06730GQA63_13695GQA64_14495GQE33_14140GQE34_09170GQE93_18180GQF59_15145GQM04_11970GQM10_14905GQM13_12280GQM17_05535GQM28_15625GRW05_06670GRW12_02500GRW27_12645GRW30_06615GRW42_09620GRW57_07945GRW80_09280GRW81_09465HmCmsJML079_03645HW43_04220PGD_03739PU06_15055WQ89_09200

Find proteins for A0A037YQ84 (Escherichia coli)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Cytoskeleton protein RodZ k57Escherichia coliMutation(s): 0 
Gene Names: rodZSAMEA3472055_00952
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    tRNA-CCA23Escherichia coli
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    MoleculeChainsLengthOrganismImage
    23S ribosomal RNAA2883Escherichia coli
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    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAB120Escherichia coli
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    f
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    A, B, b
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.10 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Swiss National Science FoundationSwitzerland--
    National Institutes of Health/National Center for Research ResourcesUnited States--

    Revision History  (Full details and data files)

    • Version 1.0: 2019-10-09
      Type: Initial release
    • Version 1.1: 2019-11-27
      Changes: Database references