3BO0

Ribosome-SecY complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ribosome binding of a single copy of the SecY complex: implications for protein translocation

Menetret, J.F.Schaletzky, J.Clemons, W.M.Osborne, A.R.Skanland, S.S.Denison, C.Gygi, S.P.Kirkpatrick, D.S.Park, E.Ludtke, S.J.Rapoport, T.A.Akey, C.W.

(2007) Mol.Cell 28: 1083-1092

  • DOI: 10.1016/j.molcel.2007.10.034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a ...

    The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a single SecY complex. The crystal structure of an archaeal SecY complex was then docked into the electron density maps. In the resulting model, two cytoplasmic loops of SecY extend into the exit tunnel near proteins L23, L29, and L24. The loop between transmembrane helices 8 and 9 interacts with helices H59 and H50 in the large subunit RNA, while the 6/7 loop interacts with H7. We also show that point mutations of basic residues within either loop abolish ribosome binding. We suggest that SecY binds to this primary site on the ribosome and subsequently captures and translocates the nascent chain.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PREPROTEIN TRANSLOCASE SecY SUBUNIT
A
442Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: secY
Find proteins for Q60175 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q60175
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PREPROTEIN TRANSLOCASE SecE SUBUNIT
B
65Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: secE
Find proteins for Q57817 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q57817
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase secG subunit
C
32Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: secG
Find proteins for P60460 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  P60460
Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAD27Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAE27Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAF19Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAG32Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance