5NCO

Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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

Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome.

Jomaa, A., Fu, Y.H., Boehringer, D., Leibundgut, M., Shan, S.O., Ban, N.

(2017) Nat Commun 8: 15470-15470

  • DOI: https://doi.org/10.1038/ncomms15470
  • Primary Citation of Related Structures:  
    5NCO

  • PubMed Abstract: 

    During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the translocon. Using electron cryo-microscopy, we have determined the structure of a quaternary complex of the translating Escherichia coli ribosome, the SRP-SR in the 'activated' state and the translocon. Our structure, supported by biochemical experiments, reveals that the SRP RNA adopts a kinked and untwisted conformation to allow repositioning of the 'activated' SRP-SR complex on the ribosome. In addition, we observe the translocon positioned through interactions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon. Our study provides new insights into the mechanism of signal sequence transfer from the SRP to the translocon.

    • 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2E [auth C]271Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3F [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4G [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5H [auth F]177Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6I [auth G]176Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9J [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10K [auth I]125Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11L [auth J]134Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13M [auth K]142Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14N [auth L]123Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15O [auth M]144Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16P [auth N]136Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17Q [auth O]125Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18R [auth P]117Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19S [auth Q]114Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20T [auth R]117Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21U [auth S]103Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22V [auth T]110Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23W [auth U]95Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24X [auth V]102Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25Y [auth W]94Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Z [auth X]76Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28AA [auth Y]77Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29BA [auth Z]62Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30CA [auth a]58Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth b]56Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33EA [auth c]51Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34FA [auth d]46Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35GA [auth e]64Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36HA [auth f]38Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecYIA [auth g]416Escherichia coliMutation(s): 0 
Gene Names: secY, prlA, b3300, JW3262
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecEJA [auth h]56Escherichia coliMutation(s): 0 
Gene Names: secE, prlG, b3981, JW3944
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle protein,Signal recognition particle proteinKA [auth i]450Escherichia coliMutation(s): 0 
Gene Names: ffh, b2610, JW5414
EC: 3.6.5.4
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-export membrane protein SecGLA [auth j]71Escherichia coliMutation(s): 0 
Gene Names: secG, b3175, JW3142
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Signal sequence (1A9L)MA [auth k]23Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle receptor FtsYNA [auth l]271Escherichia coliMutation(s): 0 
Gene Names: ftsY, b3464, JW3429
EC: 3.6.5.4
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Entity ID: 1
MoleculeChains LengthOrganismImage
4.5S SRP RNA (Ffs)A [auth 1]104Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
P-site tRNA-CCA endB [auth 2]3Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
23S rRNAC [auth A]2,903Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth B]120Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
RA [auth i],
UA [auth l]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ALF
Query on ALF
Download Ideal Coordinates CCD File 
PA [auth i],
SA [auth l]		TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
ZN
Query on ZN
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OA [auth f]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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QA [auth i],
TA [auth l]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
National Consortium for RNA and DiseaseSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2017-08-30
    Changes: Data collection
  • Version 1.4: 2018-03-28
    Changes: Structure summary