5AWW

Precise Resting State of Thermus thermophilus SecYEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  
    5CH4, 5AWW

  • 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; Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. Electronic address: ttsukaza@bs.naist.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecYY444Thermus thermophilus HB8Mutation(s): 2 
Gene Names: secYTTHA1672
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec, Translocase, and Insertase Proteins
Protein: 
SecYEG translocon, I222 space group
Find proteins for Q5SHQ8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHQ8 
Go to UniProtKB:  Q5SHQ8
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein translocase subunit SecEE60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: secETTHA0249
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec, Translocase, and Insertase Proteins
Protein: 
SecYEG translocon, I222 space group
Find proteins for P38383 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P38383 
Go to UniProtKB:  P38383
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Putative preprotein translocase, SecG subunitG75Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1784
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec, Translocase, and Insertase Proteins
Protein: 
SecYEG translocon, I222 space group
Find proteins for Q5SHE6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHE6 
Go to UniProtKB:  Q5SHE6
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.223 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.493α = 90
b = 112.904β = 90
c = 140.002γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Derived calculations