3DKN

Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.

Menetret, J.F.Hegde, R.S.Aguiar, M.Gygi, S.P.Park, E.Rapoport, T.A.Akey, C.W.

(2008) Structure 16: 1126-1137

  • DOI: 10.1016/j.str.2008.05.003

  • PubMed Abstract: 
  • During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from ...

    During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from mammalian endoplasmic reticulum in which the channel has been visualized at 11 A resolution. In this complex, single copies of Sec61 and TRAP associate with a nontranslating ribosome and this stoichiometry was verified by quantitative mass spectrometry. A bilayer-like density surrounds the channel and can be attributed to lipid and detergent. The crystal structure of an archaeal homolog of the Sec61 complex was then docked into the map. In this model, two cytoplasmic loops of Sec61 may interact with RNA helices H6, H7, and H50, while the central pore is located below the ribosome tunnel exit. Hence, this copy of Sec61 is positioned to capture and translocate the nascent chain. Finally, we show that mammalian and bacterial ribosome-channel complexes have similar architectures.


    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: 4
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit secY
A
430Methanocaldococcus 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: 5
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit secE
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: 6
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit secG
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
RNA (5'-R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*GP*C)-3')D20Canis lupus familiaris
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*CP*CP*GP*CP*AP*CP*GP*GP*AP*GP*GP*CP*GP*AP*A)-3')E17Canis lupus familiaris
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (32-MER)F32Canis lupus familiaris
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.7 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: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-07-18
    Type: Data collection