5AKA

EM structure of ribosome-SRP-FtsY complex in closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history


Literature

Ribosome-Srp-Ftsy Cotranslational Targeting Complex in the Closed State.

von Loeffelholz, O.Jiang, Q.Ariosa, A.Karuppasamy, M.Huard, K.Berger, I.Shan, S.Schaffitzel, C.

(2015) Proc Natl Acad Sci U S A 112: 3943-3948

  • DOI: 10.1073/pnas.1424453112
  • Primary Citation of Related Structures:  
    5AKA

  • PubMed Abstract: 
  • The signal recognition particle (SRP)-dependent pathway is essential for correct targeting of proteins to the membrane and subsequent insertion in the membrane or secretion. In Escherichia coli, the SRP and its receptor FtsY bind to ribosome-nascent ...

    The signal recognition particle (SRP)-dependent pathway is essential for correct targeting of proteins to the membrane and subsequent insertion in the membrane or secretion. In Escherichia coli, the SRP and its receptor FtsY bind to ribosome-nascent chain complexes with signal sequences and undergo a series of distinct conformational changes, which ensures accurate timing and fidelity of protein targeting. Initial recruitment of the SRP receptor FtsY to the SRP-RNC complex results in GTP-independent binding of the SRP-FtsY GTPases at the SRP RNA tetraloop. In the presence of GTP, a closed state is adopted by the SRP-FtsY complex. The cryo-EM structure of the closed state reveals an ordered SRP RNA and SRP M domain with a signal sequence-bound. Van der Waals interactions between the finger loop and ribosomal protein L24 lead to a constricted signal sequence-binding pocket possibly preventing premature release of the signal sequence. Conserved M-domain residues contact ribosomal RNA helices 24 and 59. The SRP-FtsY GTPases are detached from the RNA tetraloop and flexible, thus liberating the ribosomal exit site for binding of the translocation machinery.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble 38042, France; Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, European Molecular Biology Laboratory, CNRS, Grenoble 38042, France; School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom schaffitzel@embl.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32056Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33154Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35364Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE PROTEIN5109Escherichia coli K-12Mutation(s): 0 
Gene Names: ffhb2610JW5414
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA68Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2C273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3D209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4E201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5F178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6G176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9H149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11I141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13J142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14K123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15L144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 21
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50S RIBOSOMAL PROTEIN L16M136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17N127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18O117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19P114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20Q117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21R103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22S110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23T100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24U103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25V94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27W84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29X63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30Y58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31Z70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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Entity ID: 8
MoleculeChainsLengthOrganismImage
4.5S ribosomal RNA774Escherichia coli K-12
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Entity ID: 9
MoleculeChainsLengthOrganismImage
5S ribosomal RNAA120Escherichia coli K-12
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Entity ID: 10
MoleculeChainsLengthOrganismImage
23S ribosomal RNAB2904Escherichia coli K-12
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-05-06
    Changes: Other
  • Version 2.0: 2017-08-02
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2017-12-20
    Changes: Database references, Structure summary