5UWB

Re-refined 4FCZ: lipid-bound crystal structure of toluene-tolerance protein from Pseudomonas putida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4FCZ


Literature

Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.

Ekiert, D.C.Bhabha, G.Isom, G.L.Greenan, G.Ovchinnikov, S.Henderson, I.R.Cox, J.S.Vale, R.D.

(2017) Cell 169: 273-285.e17

  • DOI: https://doi.org/10.1016/j.cell.2017.03.019
  • Primary Citation of Related Structures:  
    5UVN, 5UW2, 5UW8, 5UWA, 5UWB

  • PubMed Abstract: 

    How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) protein family form hexameric assemblies with a central channel capable of mediating lipid transport. The E. coli MCE protein, MlaD, forms a ring associated with an ABC transporter complex in the inner membrane. A soluble lipid-binding protein, MlaC, ferries lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two other E. coli MCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the membranes of bacteria and some eukaryotic organelles.


  • Organizational Affiliation

    Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, The University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, The University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158, USA. Electronic address: damian.ekiert@med.nyu.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene tolerance proteinA [auth B],
B [auth A]
223Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: ttg2DPP_0961
Membrane Entity: Yes 
UniProt
Find proteins for Q88P91 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88P91 
Go to UniProtKB:  Q88P91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88P91
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth B],
B [auth A]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.868α = 90
b = 40.883β = 106.49
c = 82.399γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM112982
Damon Runyon Cancer Research FoundationUnited StatesDRG-2140-12
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Structure summary
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence