Gloeobacter Ligand-gated Ion Channel (GLIC) closed state crystallized in an ultra-swollen lipidic mesophase

Experimental Data Snapshot

  • Resolution: 6.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 

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Design of ultra-swollen lipidic mesophases for the crystallization of membrane proteins with large extracellular domains.

Zabara, A.Chong, J.T.Y.Martiel, I.Stark, L.Cromer, B.A.Speziale, C.Drummond, C.J.Mezzenga, R.

(2018) Nat Commun 9: 544-544

  • DOI: https://doi.org/10.1038/s41467-018-02996-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In meso crystallization of membrane proteins from lipidic mesophases is central to protein structural biology but limited to membrane proteins with small extracellular domains (ECDs), comparable to the water channels (3-5 nm) of the mesophase. Here we present a strategy expanding the scope of in meso crystallization to membrane proteins with very large ECDs. We combine monoacylglycerols and phospholipids to design thermodynamically stable ultra-swollen bicontinuous cubic phases of double-gyroid (Ia3d), double-diamond (Pn3m), and double-primitive (Im3m) space groups, with water channels five times larger than traditional lipidic mesophases, and showing re-entrant behavior upon increasing hydration, of sequences Ia3d→Pn3m→Ia3d and Pn3m→Im3m→Pn3m, unknown in lipid self-assembly. We use these mesophases to crystallize membrane proteins with ECDs inaccessible to conventional in meso crystallization, demonstrating the methodology on the Gloeobacter ligand-gated ion channel (GLIC) protein, and show substantial modulation of packing, molecular contacts and activation state of the ensued proteins crystals, illuminating a general strategy in protein structural biology.

  • Organizational Affiliation

    Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9 LFO E23, 8092, Zürich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-gated ion channel
A, B, C, D, E
311Gloeobacter violaceus PCC 7421Mutation(s): 0 
Gene Names: glvIglr4197
Membrane Entity: Yes 
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NDN8 
Go to UniProtKB:  Q7NDN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NDN8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 6.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.94α = 90
b = 208.22β = 90
c = 255.29γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandSinergia Grant CRSII2_154451

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description