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: https://doi.org/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. 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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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL2244Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL18B [auth D]292Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL8C [auth G]238Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL6D [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL5E [auth J]170Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL13F [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL14G [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL15H [auth N]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL13I [auth O]201Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL18J [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL19K [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL20L [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL21M [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL22N [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL14O [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL23P [auth X]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL24Q [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL27R [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL15S [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL29T [auth b]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL30U [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL31V [auth d]107Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL32W [auth e]128Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL33X [auth f]109Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL34Y [auth g]114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL29Z [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL36AA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL38BA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL39CA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL40DA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL42EA [auth o]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL3IA [auth B]394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL4JA [auth C]367Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL6KA [auth E]236Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL30LA [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL16MA [auth I]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL22NA [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL24OA [auth W]63Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL37PA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL41QA [auth n]23Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL43RA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL28SA [auth r]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL11TA [auth K]163Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL10UA [auth q]202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
SRP54VA [auth z]426Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
SRP19YA [auth 9]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
SRP68ZA [auth 6]179Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS2BB [auth SA]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS1CB [auth SB]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS5DB [auth SC]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS4EB [auth SE]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS6FB [auth SG]237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS7GB [auth SH]189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS8HB [auth SI]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS4IB [auth SJ]185Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS17JB [auth SL]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS15KB [auth SN]149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS11LB [auth SO]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS21MB [auth SV]82Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS8NB [auth SW]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS12OB [auth SX]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS24PB [auth SY]126Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS26QB [auth Sa]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS27RB [auth Sb]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS30SB [auth Se]57Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS3TB [auth SD]227Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS7UB [auth SF]191Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS10VB [auth SK]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS12WB [auth SM]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS19XB [auth SP]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS9YB [auth SQ]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS17ZB [auth SR]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS13AC [auth SS]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS19BC [auth ST]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS10CC [auth SU]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein es25DC [auth SZ]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS28EC [auth Sc]64Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS14FC [auth Sd]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS31GC [auth Sf]71Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein RACK1HC [auth Sg]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
SRP9IC [auth S1]74Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
SRP14JC [auth S4]76Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains LengthOrganismImage
28S ribosomal RNAFA [auth 5]3,658Oryctolagus cuniculus
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Entity ID: 33
MoleculeChains LengthOrganismImage
5S ribosomal RNAGA [auth 7]120Oryctolagus cuniculus
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Entity ID: 34
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAHA [auth 8]156Oryctolagus cuniculus
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Entity ID: 49
MoleculeChains LengthOrganismImage
Val tRNAWA [auth 3]76Oryctolagus cuniculus
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Entity ID: 50
MoleculeChains LengthOrganismImage
SRP 7S RNAXA [auth 4]206Oryctolagus cuniculus
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Entity ID: 53
MoleculeChains LengthOrganismImage
18S ribosomal RNAAB [auth S2]1,742Oryctolagus cuniculus
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MH [auth j],
NC [auth m],
OC [auth o],
XI [auth Sa]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth 5]
AE [auth 5]
AF [auth 5]
AG [auth 5]
AH [auth 5]
AD [auth 5],
AE [auth 5],
AF [auth 5],
AG [auth 5],
AH [auth 5],
AI [auth S2],
BD [auth 5],
BE [auth 5],
BF [auth 5],
BG [auth 5],
BH [auth 7],
BI [auth S2],
CD [auth 5],
CE [auth 5],
CF [auth 5],
CG [auth 5],
CH [auth 7],
CI [auth S2],
DD [auth 5],
DE [auth 5],
DF [auth 5],
DG [auth 5],
DH [auth 7],
DI [auth S2],
ED [auth 5],
EE [auth 5],
EF [auth 5],
EG [auth 5],
EH [auth 7],
EI [auth S2],
FD [auth 5],
FE [auth 5],
FF [auth 5],
FG [auth 5],
FH [auth 7],
FI [auth S2],
GD [auth 5],
GE [auth 5],
GF [auth 5],
GG [auth 5],
GH [auth 8],
GI [auth S2],
HD [auth 5],
HE [auth 5],
HF [auth 5],
HG [auth 5],
HH [auth 8],
HI [auth S2],
ID [auth 5],
IE [auth 5],
IF [auth 5],
IG [auth 5],
IH [auth 8],
II [auth S2],
JD [auth 5],
JE [auth 5],
JF [auth 5],
JG [auth 5],
JH [auth 8],
JI [auth S2],
KC [auth D],
KD [auth 5],
KE [auth 5],
KF [auth 5],
KG [auth 5],
KH [auth 8],
KI [auth S2],
LC [auth V],
LD [auth 5],
LE [auth 5],
LF [auth 5],
LG [auth 5],
LH [auth 8],
LI [auth S2],
MC [auth g],
MD [auth 5],
ME [auth 5],
MF [auth 5],
MG [auth 5],
MI [auth S2],
ND [auth 5],
NE [auth 5],
NF [auth 5],
NG [auth 5],
NH [auth S2],
NI [auth S2],
OD [auth 5],
OE [auth 5],
OF [auth 5],
OG [auth 5],
OH [auth S2],
OI [auth S2],
PC [auth 5],
PD [auth 5],
PE [auth 5],
PF [auth 5],
PG [auth 5],
PH [auth S2],
PI [auth S2],
QC [auth 5],
QD [auth 5],
QE [auth 5],
QF [auth 5],
QG [auth 5],
QH [auth S2],
QI [auth S2],
RC [auth 5],
RD [auth 5],
RE [auth 5],
RF [auth 5],
RG [auth 5],
RH [auth S2],
RI [auth S2],
SC [auth 5],
SD [auth 5],
SE [auth 5],
SF [auth 5],
SG [auth 5],
SH [auth S2],
SI [auth S2],
TC [auth 5],
TD [auth 5],
TE [auth 5],
TF [auth 5],
TG [auth 5],
TH [auth S2],
TI [auth S2],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth 5],
UG [auth 5],
UH [auth S2],
UI [auth S2],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth 5],
VG [auth 5],
VH [auth S2],
VI [auth S2],
WC [auth 5],
WD [auth 5],
WE [auth 5],
WF [auth 5],
WG [auth 5],
WH [auth S2],
WI [auth S2],
XC [auth 5],
XD [auth 5],
XE [auth 5],
XF [auth 5],
XG [auth 5],
XH [auth S2],
YC [auth 5],
YD [auth 5],
YE [auth 5],
YF [auth 5],
YG [auth 5],
YH [auth S2],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5],
ZF [auth 5],
ZG [auth 5],
ZH [auth S2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 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: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-12-30
    Changes: Database references