5AWW

Precise Resting State of Thermus thermophilus SecYEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.724 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State.

Tanaka, Y.Sugano, Y.Takemoto, M.Mori, T.Furukawa, A.Kusakizako, T.Kumazaki, K.Kashima, A.Ishitani, R.Sugita, Y.Nureki, O.Tsukazaki, T.

(2015) Cell Rep 13: 1561-1568

  • DOI: 10.1016/j.celrep.2015.10.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bacterial SecYEG translocon functions as a conserved protein-conducting channel. Conformational transitions of SecYEG allow protein translocation across the membrane without perturbation of membrane permeability. Here, we report the crystal struc ...

    The bacterial SecYEG translocon functions as a conserved protein-conducting channel. Conformational transitions of SecYEG allow protein translocation across the membrane without perturbation of membrane permeability. Here, we report the crystal structures of intact SecYEG at 2.7-Å resolution and of peptide-bound SecYEG at 3.6-Å resolution. The higher-resolution structure revealed that the cytoplasmic loop of SecG covers the hourglass-shaped channel, which was confirmed to also occur in the membrane by disulfide bond formation analysis and molecular dynamics simulation. The cytoplasmic loop may be involved in protein translocation. In addition, the previously unknown peptide-bound crystal structure of SecYEG implies that interactions between the cytoplasmic side of SecY and signal peptides are related to lateral gate opening at the first step of protein translocation. These SecYEG structures therefore provide a number of structural insights into the Sec machinery for further study.


    Organizational Affiliation

    Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecY
Y
444Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 2 
Gene Names: secY
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec and Translocase Proteins
Protein: 
SecYE translocon in complex with a Fab fragment
Find proteins for Q5SHQ8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecE
E
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: secE
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec and Translocase Proteins
Protein: 
SecYE translocon in complex with a Fab fragment
Find proteins for P38383 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P38383
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Putative preprotein translocase, SecG subunit
G
75Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec and Translocase Proteins
Protein: 
SecYE translocon in complex with a Fab fragment
Find proteins for Q5SHE6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHE6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
G, Y
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.724 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.493α = 90.00
b = 112.904β = 90.00
c = 140.002γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references