3JAN

Structure of the scanning state of the mammalian SRP-ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 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

Structures of the scanning and engaged states of the mammalian SRP-ribosome complex.

Voorhees, R.M.Hegde, R.S.

(2015) Elife 4

  • DOI: 10.7554/eLife.07975
  • Primary Citation of Related Structures:  
    3JAJ, 3JAN

  • PubMed Abstract: 
  • The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane ...

    The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules

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Ribosomal protein uL2 A244Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uL18 D292Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eL8 G238Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uL6 H190Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uL5 J170Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eL13 L210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
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SRP54 z426Oryctolagus cuniculusMutation(s): 0 
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SRP19 9105Oryctolagus cuniculusMutation(s): 0 
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SRP68 6179Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS4 SE262Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS6 SG237Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS21 SV82Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uS12 SX141Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS24 SY126Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS26 Sa98Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uS3 SD227Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uS7 SF191Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS12 SM124Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uS19 SP96Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uS9 SQ141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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Ribosomal protein eS17 SR129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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Ribosomal protein uS13 SS137Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS19 ST141Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uS10 SU104Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein es25 SZ75Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS28 Sc64Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein uS14 Sd52Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein eS31 Sf71Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein RACK1 Sg313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 87
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SRP9 S174Oryctolagus cuniculusMutation(s): 0 
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SRP14 S476Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsLengthOrganismImage
28S ribosomal RNA53658Oryctolagus cuniculus
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Entity ID: 33
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5S ribosomal RNA7120Oryctolagus cuniculus
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5.8S ribosomal RNA8156Oryctolagus cuniculus
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MoleculeChainsLengthOrganismImage
Val tRNA376Oryctolagus cuniculus
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Entity ID: 50
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SRP 7S RNA4206Oryctolagus cuniculus
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Entity ID: 53
MoleculeChainsLengthOrganismImage
18S ribosomal RNAS21742Oryctolagus cuniculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Sa, j, m, o
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
5, 7, 8, D, S2, V, g
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-12-30
    Changes: Database references