6B21

Crystal structure of AmtB from E. coli bound to TopFluor cardiolipin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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This is version 1.5 of the entry. See complete history


Literature

Allostery revealed within lipid binding events to membrane proteins.

Patrick, J.W.Boone, C.D.Liu, W.Conover, G.M.Liu, Y.Cong, X.Laganowsky, A.

(2018) Proc Natl Acad Sci U S A 115: 2976-2981

  • DOI: https://doi.org/10.1073/pnas.1719813115
  • Primary Citation of Related Structures:  
    6B21

  • PubMed Abstract: 

    Membrane proteins interact with a myriad of lipid species in the biological membrane, leading to a bewildering number of possible protein-lipid assemblies. Despite this inherent complexity, the identification of specific protein-lipid interactions and the crucial role of lipids in the folding, structure, and function of membrane proteins is emerging from an increasing number of reports. Fundamental questions remain, however, regarding the ability of specific lipid binding events to membrane proteins to alter remote binding sites for lipids of a different type, a property referred to as allostery [Monod J, Wyman J, Changeux JP (1965) J Mol Biol 12:88-118]. Here, we use native mass spectrometry to determine the allosteric nature of heterogeneous lipid binding events to membrane proteins. We monitored individual lipid binding events to the ammonia channel (AmtB) from Escherichia coli , enabling determination of their equilibrium binding constants. We found that different lipid pairs display a range of allosteric modulation. In particular, the binding of phosphatidylethanolamine and cardiolipin-like molecules to AmtB exhibited the largest degree of allosteric modulation, inspiring us to determine the cocrystal structure of AmtB in this lipid environment. The 2.45-Å resolution structure reveals a cardiolipin-like molecule bound to each subunit of the trimeric complex. Mutation of a single residue in AmtB abolishes the positive allosteric modulation observed for binding phosphatidylethanolamine and cardiolipin-like molecules. Our results demonstrate that specific lipid-protein interactions can act as allosteric modulators for the binding of different lipid types to integral membrane proteins.


  • Organizational Affiliation

    Department of Chemistry, Texas A&M University, College Station, TX 77842.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonia channel406Escherichia coli K-12Mutation(s): 0 
Gene Names: amtBybaGb0451JW0441
Membrane Entity: Yes 
UniProt
Find proteins for P69681 (Escherichia coli (strain K12))
Explore P69681 
Go to UniProtKB:  P69681
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69681
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C9V
Query on C9V

Download Ideal Coordinates CCD File 
B [auth A][(2R,5R,11R,14S,24E)-14-[(acetyloxy)methyl]-8-{[5-(3,5-dimethyl-1H-pyrrol-2-yl-kappaN)-5-(3,5-dimethyl-2H-pyrrol-2-ylidene-kappaN)pentanoyl]oxy}-5,11-dihydroxy-2-{[(9E)-octadec-9-enoyl]oxy}-5,11,16-trioxo-4,6,10,12,15-pentaoxa-5lambda~5~,11lambda~5~-diphosphatritriacont-24-en-1-yl (9E)-octadec-9-enoatato](difluoro)boron
C82 H139 B F2 N2 O18 P2
GDYLGRNGCDWDQL-UUEIIFSHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.78α = 90
b = 138.78β = 90
c = 159.14γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM123486

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Derived calculations
  • Version 1.2: 2018-03-21
    Changes: Database references
  • Version 1.3: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description