5GAF

RNC in complex with SRP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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 E. coli translating ribosome with SRP and its receptor and with the translocon

Jomaa, A.Boehringer, D.Leibundgut, M.Ban, N.

(2016) Nat Commun 7: 10471-10471

  • DOI: 10.1038/ncomms10471
  • Primary Citation of Related Structures:  
    5GAH, 5GAG, 5GAD, 5GAF, 5GAE

  • PubMed Abstract: 
  • Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here we present snapshots of key co-translational-targeting complexes solved by cryo-electron microscopy at near-atomic resolution, establishing the molecular contacts between the Escherichia coli translating ribosome, the signal recognition particle and the translocon ...

    Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here we present snapshots of key co-translational-targeting complexes solved by cryo-electron microscopy at near-atomic resolution, establishing the molecular contacts between the Escherichia coli translating ribosome, the signal recognition particle and the translocon. Our results reveal the conformational changes that regulate the latching of the signal sequence, the release of the heterodimeric domains of the signal recognition particle and its receptor, and the handover of the signal sequence to the translocon. We also observe that the signal recognition particle and the translocon insert-specific structural elements into the ribosomal tunnel to remodel it, possibly to sense nascent chains. Our work provides structural evidence for a conformational state of the signal recognition particle and its receptor primed for translocon binding to the ribosome-nascent chain complex.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich CH-8093, Switzerland.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 C271Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 D209Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 E201Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 F177Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 G176Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 H149Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10 I125Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L11 J134Escherichia coliMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L13 K142Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L14 L123Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L15 M144Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L16 N136Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 O125Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L18 P117Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L19 Q114Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L20 R117Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21 S103Escherichia coliMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L22 T110Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L23 U95Escherichia coliMutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L24 V102Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L25 W94Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L27 X76Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L28 Y77Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L29 Z62Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L30 a58Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 b56Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L33 c51Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 d46Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L35 e64Escherichia coliMutation(s): 0 
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Entity ID: 34
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50S ribosomal protein L36 f38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle protein i398Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
1A9L SS k18Escherichia coliMutation(s): 0 
EC: 3.1.3.1
Find proteins for P00634 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SRP 4.5S RNA1113Escherichia coli
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    tRNA CCAend23Escherichia coli
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    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNAA2883Escherichia coli
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    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAB120Escherichia coli
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP

    Download Ideal Coordinates CCD File 
    i
    PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    f
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    2, A, B, C, D, E, P, R, b
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.30 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2016-02-03
      Type: Initial release
    • Version 1.1: 2016-02-10
      Changes: Structure summary
    • Version 1.2: 2017-07-05
      Changes: Database references
    • Version 1.3: 2017-08-02
      Changes: Data collection, Derived calculations
    • Version 1.4: 2019-12-11
      Changes: Advisory, Derived calculations, Other