5CH4

Peptide-Bound State of Thermus thermophilus SecYEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.257 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.celrep.2015.10.025
  • Primary Citation of Related Structures:  
    5AWW, 5CH4

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecYA [auth Y]441Thermus thermophilus HB8Mutation(s): 4 
Gene Names: secYTTHA1672
Membrane Entity: Yes 
UniProt
Find proteins for Q5SHQ8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHQ8 
Go to UniProtKB:  Q5SHQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHQ8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein translocase subunit SecEB [auth E]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: secETTHA0249
Membrane Entity: Yes 
UniProt
Find proteins for P38383 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P38383 
Go to UniProtKB:  P38383
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38383
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative preprotein translocase, SecG subunitC [auth G]75Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1784
Membrane Entity: Yes 
UniProt
Find proteins for Q5SHE6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHE6 
Go to UniProtKB:  Q5SHE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHE6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.829α = 90
b = 138.007β = 90
c = 115.974γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata collection
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description