4D65

Structure of porin Omp-Pst2 from P. stuartii; the asymmetric unit contains a dimer of trimers.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.197 (Depositor) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.168 (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 FTTClick on this verticalbar to view detailsBest fitted LDAClick on this verticalbar to view detailsBest fitted MYRClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Porin self-association enables cell-to-cell contact inProvidencia stuartiifloating communities.

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 2
A, B, C, D, E
343Providencia stuartiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E3U905 (Providencia stuartii)
Explore E3U905 
Go to UniProtKB:  E3U905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3U905
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTT
Query on FTT

Download Ideal Coordinates CCD File 
ED [auth C]
GD [auth C]
HC [auth B]
ID [auth C]
KD [auth C]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
LDA
Query on LDA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth C]
AE [auth D]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
FD [auth C]
HD [auth C]
IC [auth B]
JD [auth C]
LD [auth C]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
MD [auth C],
ME [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.197 (Depositor) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.26α = 90
b = 135.51β = 114.61
c = 151.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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 FTTClick on this verticalbar to view detailsBest fitted LDAClick on this verticalbar to view detailsBest fitted MYRClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description