5O2Y | pdb_00005o2y

NMR structure of the calcium bound form of PulG, major pseudopilin from Klebsiella oxytoca T2SS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

Validation slider image for 5O2Y

This is version 1.3 of the entry. See complete history

Literature

Structure of the calcium-dependent type 2 secretion pseudopilus.

Lopez-Castilla, A.Thomassin, J.L.Bardiaux, B.Zheng, W.Nivaskumar, M.Yu, X.Nilges, M.Egelman, E.H.Izadi-Pruneyre, N.Francetic, O.

(2017) Nat Microbiol 2: 1686-1695

  • DOI: https://doi.org/10.1038/s41564-017-0041-2
  • Primary Citation Related Structures: 
    5O2Y, 5WDA

  • PubMed Abstract: 

    Many Gram-negative bacteria use type 2 secretion systems (T2SSs) to secrete proteins involved in virulence and adaptation. Transport of folded proteins via T2SS nanomachines requires the assembly of inner membrane-anchored fibres called pseudopili. Although efficient pseudopilus assembly is essential for protein secretion, structure-based functional analyses are required to unravel the mechanistic link between these processes. Here, we report an atomic model for a T2SS pseudopilus from Klebsiella oxytoca, obtained by fitting the NMR structure of its calcium-bound subunit PulG into the ~5-Å-resolution cryo-electron microscopy reconstruction of assembled fibres. This structure reveals the comprehensive network of inter-subunit contacts and unexpected features, including a disordered central region of the PulG helical stem, and highly flexible C-terminal residues on the fibre surface. NMR, mutagenesis and functional analyses highlight the key role of calcium in PulG folding and stability. Fibre disassembly in the absence of calcium provides a basis for pseudopilus length control, essential for protein secretion, and supports the Archimedes screw model for the type 2 secretion mechanism.


  • Organizational Affiliation
    • NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 28 rue du Dr Roux, 75724, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 12.97 kDa 
  • Atom Count: 914 
  • Modeled Residue Count: 116 
  • Deposited Residue Count: 116 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
General secretion pathway protein G116Klebsiella oxytocaMutation(s): 0 
Gene Names: pulGAB185_31145SAMEA2273639_02747

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE09-0004NR

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references