5WQ7

CryoEM structure of type II secretion system secretin GspD in E.coli K12


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the secretin translocation channel in the type II secretion system

Yan, Z.Yin, M.Xu, D.Zhu, Y.Li, X.

(2017) Nat. Struct. Mol. Biol. 24: 177-183

  • DOI: 10.1038/nsmb.3350
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. The lack of an atomic-resolution structure of the Gsp ...

    The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. The lack of an atomic-resolution structure of the GspD channel hinders the investigation of substrate translocation mechanism of T2SS. Here we report cryo-EM structures of two GspD channels (∼1 MDa), from Escherichia coli K12 and Vibrio cholerae, at ∼3 Å resolution. The structures reveal a pentadecameric channel architecture, wherein three rings of GspD N domains form the periplasmic channel. The secretin domain constitutes a novel double β-barrel channel, with at least 60 β-strands in each barrel, and is stabilized by S domains. The outer membrane channel is sealed by β-strand-enriched gates. On the basis of the partially open state captured, we proposed a detailed gate-opening mechanism. Our structures provide a structural basis for understanding the secretin superfamily and the mechanism of substrate translocation in T2SS.


    Organizational Affiliation

    Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative type II secretion system protein D
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
627Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gspD (yheF)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Type II Secretion Systems
Protein: 
GspD secretin
Find proteins for P45758 (Escherichia coli (strain K12))
Go to UniProtKB:  P45758
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-11-23 
  • Released Date: 2016-12-28 
  • Deposition Author(s): Yan, Z., Yin, M., Li, X.

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-02-22
    Type: Database references
  • Version 1.3: 2019-10-16
    Type: Data collection, Other