3DL8

Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.5 Å
  • R-Value Free: 0.390 
  • R-Value Work: 0.365 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a complex of the ATPase SecA and the protein-translocation channel.

Zimmer, J.Nam, Y.Rapoport, T.A.

(2008) Nature 455: 936-943

  • DOI: 10.1038/nature07335
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Most proteins are secreted from bacteria by the interaction of the cytoplasmic SecA ATPase with a membrane channel, formed by the heterotrimeric SecY complex. Here we report the crystal structure of SecA bound to the SecY complex, with a maximum reso ...

    Most proteins are secreted from bacteria by the interaction of the cytoplasmic SecA ATPase with a membrane channel, formed by the heterotrimeric SecY complex. Here we report the crystal structure of SecA bound to the SecY complex, with a maximum resolution of 4.5 ångström (A), obtained for components from Thermotoga maritima. One copy of SecA in an intermediate state of ATP hydrolysis is bound to one molecule of the SecY complex. Both partners undergo important conformational changes on interaction. The polypeptide-cross-linking domain of SecA makes a large conformational change that could capture the translocation substrate in a 'clamp'. Polypeptide movement through the SecY channel could be achieved by the motion of a 'two-helix finger' of SecA inside the cytoplasmic funnel of SecY, and by the coordinated tightening and widening of SecA's clamp above the SecY pore. SecA binding generates a 'window' at the lateral gate of the SecY channel and it displaces the plug domain, preparing the channel for signal sequence binding and channel opening.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit secA
A, B
779Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: secA (div+)
Find proteins for P28366 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P28366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit secY
G, H
429Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: secY
Find proteins for O66491 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66491
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SecE
C, D
65Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: secE
Find proteins for D0VWU4 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  D0VWU4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein-export membrane protein secG
E, F
107Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: secG
Find proteins for O66505 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66505
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.5 Å
  • R-Value Free: 0.390 
  • R-Value Work: 0.365 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 146.359α = 90.00
b = 167.974β = 90.00
c = 187.722γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-25
    Type: Derived calculations