5EUL

Structure of the SecA-SecY complex with a translocating polypeptide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a substrate-engaged SecY protein-translocation channel.

Li, L.Park, E.Ling, J.Ingram, J.Ploegh, H.Rapoport, T.A.

(2016) Nature 531: 395-399

  • DOI: 10.1038/nature17163

  • PubMed Abstract: 
  • Hydrophobic signal sequences target secretory polypeptides to a protein-conducting channel formed by a heterotrimeric membrane protein complex, the prokaryotic SecY or eukaryotic Sec61 complex. How signal sequences are recognized is poorly understood ...

    Hydrophobic signal sequences target secretory polypeptides to a protein-conducting channel formed by a heterotrimeric membrane protein complex, the prokaryotic SecY or eukaryotic Sec61 complex. How signal sequences are recognized is poorly understood, particularly because they are diverse in sequence and length. Structures of the inactive channel show that the largest subunit, SecY or Sec61α, consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces lipid. The cytoplasmic funnel is empty, while the extracellular funnel is filled with a plug domain. In bacteria, the SecY channel associates with the translating ribosome in co-translational translocation, and with the SecA ATPase in post-translational translocation. How a translocating polypeptide inserts into the channel is uncertain, as cryo-electron microscopy structures of the active channel have a relatively low resolution (~10 Å) or are of insufficient quality. Here we report a crystal structure of the active channel, assembled from SecY complex, the SecA ATPase, and a segment of a secretory protein fused into SecA. The translocating protein segment inserts into the channel as a loop, displacing the plug domain. The hydrophobic core of the signal sequence forms a helix that sits in a groove outside the lateral gate, while the following polypeptide segment intercalates into the gate. The carboxy (C)-terminal section of the polypeptide loop is located in the channel, surrounded by residues of the pore ring. Thus, during translocation, the hydrophobic segments of signal sequences, and probably bilayer-spanning domains of nascent membrane proteins, exit the lateral gate and dock at a specific site that faces the lipid phase.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecA, Insertion Peptide Chimera
A
836Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: secA (div+)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec and Translocase Proteins
Protein: 
SecYE translocon in complex with B. subtilis SecA
Find proteins for P28366 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P28366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecY
Y
424Geobacillus thermodenitrificans (strain NG80-2)Mutation(s): 0 
Gene Names: secY
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sec and Translocase Proteins
Protein: 
SecYE translocon in complex with B. subtilis SecA
Find proteins for A4IJK8 (Geobacillus thermodenitrificans (strain NG80-2))
Go to UniProtKB:  A4IJK8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase SecE subunit
E
70Geobacillus thermodenitrificans (strain NG80-2)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 B. subtilis SecA
Find proteins for A4IJH4 (Geobacillus thermodenitrificans (strain NG80-2))
Go to UniProtKB:  A4IJH4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
AYC08
V
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TBR
Query on TBR

Download SDF File 
Download CCD File 
A, Y
HEXATANTALUM DODECABROMIDE
DODECABROMOHEXATANTALUM
Br12 Ta6
YWYIQTPPCOBSGN-UHFFFAOYSA-M
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.295 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 127.798α = 90.00
b = 127.798β = 90.00
c = 554.772γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM052586

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2016-03-30
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations