3J45

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.5 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:  

  • 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 ch ...

    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

    School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Department of Cell Biology and Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.,Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118-2526, USA.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecY
y
437Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secY (prlA)
Find proteins for P0AGA2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGA2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit SecE
E
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secE (prlG)
Find proteins for P0AG96 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG96
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein-export membrane protein SecG
G
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: secG
Find proteins for P0AG99 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG99
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 7
MoleculeChainsLengthOrganism
23S ribosomal RNA163Escherichia coli
Entity ID: 8
MoleculeChainsLengthOrganism
23S ribosomal RNA236Escherichia coli
Entity ID: 9
MoleculeChainsLengthOrganism
23S ribosomal RNA318Escherichia coli
Entity ID: 10
MoleculeChainsLengthOrganism
23S ribosomal RNA461Escherichia coli
Entity ID: 11
MoleculeChainsLengthOrganism
23S ribosomal RNA5108Escherichia coli
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
E, y
NON-POLYMERH2 N

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ACE
Query on ACE
E, y
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-06
    Type: Database references
  • Version 1.2: 2014-02-05
    Type: Database references
  • Version 1.3: 2018-07-18
    Type: Data collection