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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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 Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118-2526, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecYA [auth y]437Escherichia coliMutation(s): 2 
Gene Names: secY
Find proteins for P0AGA2 (Escherichia coli (strain K12))
Explore P0AGA2 
Go to UniProtKB:  P0AGA2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Preprotein translocase subunit SecEB [auth E]56Escherichia coliMutation(s): 2 
Gene Names: secE
Find proteins for P0AG96 (Escherichia coli (strain K12))
Explore P0AG96 
Go to UniProtKB:  P0AG96
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-export membrane protein SecGC [auth G]65Escherichia coliMutation(s): 0 
Gene Names: secG
Find proteins for P0AG99 (Escherichia coli (strain K12))
Explore P0AG99 
Go to UniProtKB:  P0AG99
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23D [auth T]100Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Explore P0ADZ0 
Go to UniProtKB:  P0ADZ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24E [auth U]103Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
Explore P60624 
Go to UniProtKB:  P60624
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29F [auth Y]63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
Go to UniProtKB:  P0A7M6
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
23S ribosomal RNAG [auth 1]63Escherichia coli
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsLengthOrganismImage
23S ribosomal RNAH [auth 2]36Escherichia coli
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 9
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNAI [auth 3]18Escherichia coli
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 10
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNAJ [auth 4]61Escherichia coli
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 11
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNAK [auth 5]108Escherichia coli
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 9.50 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: 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