3BO0

Ribosome-SecY complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.60 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: https://doi.org/10.1016/j.molcel.2007.10.034
  • Primary Citation of Related Structures:  
    3BO0, 3BO1

  • 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 single SecY complex ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PREPROTEIN TRANSLOCASE SecY SUBUNITE [auth A]442Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q60175 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q60175 
Go to UniProtKB:  Q60175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60175
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PREPROTEIN TRANSLOCASE SecE SUBUNITF [auth B]65Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q57817 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57817 
Go to UniProtKB:  Q57817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57817
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Preprotein translocase secG subunitG [auth C]32Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P60460 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore P60460 
Go to UniProtKB:  P60460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60460
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAA [auth D]27Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAB [auth E]27Escherichia coli
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAC [auth F]19Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAD [auth G]32Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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