5NXR

Trimeric structure of Omp-Pst1, the major porin from Providencia stuartii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.285 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LDAClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

Porin self-association enables cell-to-cell contact in

El-Khatib, M.Nasrallah, C.Lopes, J.Tran, Q.T.Tetreau, G.Basbous, H.Fenel, D.Gallet, B.Lethier, M.Bolla, J.M.Pages, J.M.Vivaudou, M.Weik, M.Winterhalter, M.Colletier, J.P.

(2018) Proc Natl Acad Sci U S A 115: E2220-E2228

  • DOI: https://doi.org/10.1073/pnas.1714582115
  • Primary Citation of Related Structures:  
    4D64, 4D65, 5N9H, 5N9I, 5NXN, 5NXR, 5NXU

  • PubMed Abstract: 

    The gram-negative pathogen Providencia stuartii forms floating communities within which adjacent cells are in apparent contact, before depositing as canonical surface-attached biofilms. Because porins are the most abundant proteins in the outer membrane of gram-negative bacteria, we hypothesized that they could be involved in cell-to-cell contact and undertook a structure-function relationship study on the two porins of P. stuartii , Omp-Pst1 and Omp-Pst2. Our crystal structures reveal that these porins can self-associate through their extracellular loops, forming dimers of trimers (DOTs) that could enable cell-to-cell contact within floating communities. Support for this hypothesis was obtained by studying the porin-dependent aggregation of liposomes and model cells. The observation that facing channels are open in the two porin structures suggests that DOTs could not only promote cell-to-cell contact but also contribute to intercellular communication.


  • Organizational Affiliation

    Institut de Biologie Structurale (IBS), University of Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 38000 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Porin 1A,
B [auth C],
C [auth B]
352Providencia stuartiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E3U904 (Providencia stuartii)
Explore E3U904 
Go to UniProtKB:  E3U904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3U904
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth C]
BA [auth C]
BB [auth C]
CA [auth C]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
Q [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
R [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.285 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.84α = 90
b = 129β = 90
c = 159.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LDAClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05-02
French National Research AgencyFranceANR-10-LABX-49-01
French National Research AgencyFranceANR-15-CE18-0005-02

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 2.0: 2019-02-06
    Changes: Advisory, Atomic model, Data collection
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description