5D6I

DgkA - CIM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.091 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The cubicon method for concentrating membrane proteins in the cubic mesophase.

Ma, P.Weichert, D.Aleksandrov, L.A.Jensen, T.J.Riordan, J.R.Liu, X.Kobilka, B.K.Caffrey, M.

(2017) Nat Protoc 12: 1745-1762

  • DOI: 10.1038/nprot.2017.057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The lipid cubic phase (in meso) method is an important approach for generating crystals and high-resolution X-ray structures of integral membrane proteins. However, as a consequence of instability, it can be impossible-using traditional methods-to co ...

    The lipid cubic phase (in meso) method is an important approach for generating crystals and high-resolution X-ray structures of integral membrane proteins. However, as a consequence of instability, it can be impossible-using traditional methods-to concentrate certain membrane proteins and complexes to values suitable for in meso crystallization and structure determination. The cubicon method described here exploits the amphiphilic nature of membrane proteins and their natural tendency to partition preferentially into lipid bilayers from aqueous solution. Using several rounds of reconstitution, the protein concentration in the bilayer of the cubic mesophase can be ramped up stepwise from less than a milligram per milliliter to tens of milligrams per milliliter for crystallogenesis. The general applicability of the method is demonstrated with five integral membrane proteins: the β 2 -adrenergic G protein-coupled receptor (β 2 AR), the peptide transporter (PepT St ), diacylglycerol kinase (DgkA), the alginate transporter (AlgE) and the cystic fibrosis transmembrane conductance regulator (CFTR). In the cases of β 2 AR, PepT St , DgkA and AlgE, an effective 20- to 45-fold concentration was realized, resulting in a protein-laden mesophase that allowed the formation of crystals using the in meso method and structure determination to resolutions ranging from 2.4 Å to 3.2 Å. In addition to opening up in meso crystallization to a broader range of integral membrane protein targets, the cubicon method should find application in situations that require membrane protein reconstitution in a lipid bilayer at high concentrations. These applications include functional and biophysical characterization studies for ligand screening, drug delivery, antibody production and protein complex formation. A typical cubicon experiment can be completed in 3-5 h.


    Organizational Affiliation

    Department of Biochemistry and Biophysics and Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.,Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China.,Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diacylglycerol kinase
A, B, C
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dgkA
EC: 2.7.1.107
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABN1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.091 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.266 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.765α = 90.00
b = 72.765β = 90.00
c = 199.650γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-12 
  • Released Date: 2016-08-17 
  • Deposition Author(s): Ma, P., Caffrey, M.

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255
Belgian National Funds for Scientific ResearchBelgiumWELBIO CR-2012S-04

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references