3J45

Structure of a non-translocating SecY protein channel with the 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structure of the SecY channel during initiation of protein translocation.

Park, E.Menetret, J.F.Gumbart, J.C.Ludtke, S.J.Li, W.Whynot, A.Rapoport, T.A.Akey, C.W.

(2013) Nature 506: 102-106

  • DOI: https://doi.org/10.1038/nature12720
  • Primary Citation of Related Structures:  
    3J45, 3J46, 4V4N

  • PubMed Abstract: 

    Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome-nascent chain complex binds to the SecY (or Sec61) complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here we have addressed this question by determining structures of inactive and active ribosome-channel complexes with cryo-electron microscopy. Non-translating ribosome-SecY channel complexes derived from Methanocaldococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome-channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the amino- and carboxy-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than entering the channel directly.


  • Organizational Affiliation

    Department of Cell Biology and Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecYA [auth y]437Escherichia coliMutation(s): 2 
Gene Names: secY
Membrane Entity: Yes 
UniProt
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UniProt GroupP0AGA2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Preprotein translocase subunit SecEB [auth E]56Escherichia coliMutation(s): 2 
Gene Names: secE
Membrane Entity: Yes 
UniProt
Find proteins for P0AG96 (Escherichia coli (strain K12))
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UniProt GroupP0AG96
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-export membrane protein SecGC [auth G]65Escherichia coliMutation(s): 0 
Gene Names: secG
Membrane Entity: Yes 
UniProt
Find proteins for P0AG99 (Escherichia coli (strain K12))
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UniProt GroupP0AG99
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23D [auth T]100Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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UniProt GroupP0ADZ0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24E [auth U]103Escherichia coliMutation(s): 0 
UniProt
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UniProt GroupP60624
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29F [auth Y]63Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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UniProt GroupP0A7M6
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Entity ID: 7
MoleculeChains LengthOrganismImage
23S ribosomal RNAG [auth 1]63Escherichia coli
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Entity ID: 8
MoleculeChains LengthOrganismImage
23S ribosomal RNAH [auth 2]36Escherichia coli
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Entity ID: 9
MoleculeChains LengthOrganismImage
23S ribosomal RNAI [auth 3]18Escherichia coli
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S ribosomal RNAJ [auth 4]61Escherichia coli
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Entity ID: 11
MoleculeChains LengthOrganismImage
23S ribosomal RNAK [auth 5]108Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN1

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-27
    Changes: Structure summary