5VN7

Structure of bacteriorhodopsin from crystals grown at 20 deg Celcius using GlyNCOC15+4 as an LCP host lipid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Chemically Stable Lipids for Membrane Protein Crystallization.

Ishchenko, A.Peng, L.Zinovev, E.Vlasov, A.Lee, S.C.Kuklin, A.Mishin, A.Borshchevskiy, V.Zhang, Q.Cherezov, V.

(2017) Cryst Growth Des 17: 3502-3511

  • DOI: https://doi.org/10.1021/acs.cgd.7b00458
  • Primary Citation of Related Structures:  
    5VN7, 5VN9

  • PubMed Abstract: 

    Lipidic cubic phase (LCP) has been widely recognized as a promising membrane-mimicking matrix for biophysical studies of membrane proteins and their crystallization in a lipidic environment. Application of this material to a wide variety of membrane proteins, however, is hindered due to a limited number of available host lipids, mostly monoacylglycerols (MAGs). Here, we designed, synthesized and characterized a series of chemically stable lipids resistant to hydrolysis, with properties complementary to the widely used MAGs. In order to assess their potential to serve as host lipids for crystallization, we characterized the phase properties and lattice parameters of mesophases made of two most promising lipids at a variety of different conditions by polarized light microscopy and small-angle X-ray scattering. Both lipids showed remarkable chemical stability and an extended LCP region in the phase diagram covering a wide range of temperatures down to 4 °C. One of these lipids has been used for crystallization and structure determination of a prototypical membrane protein bacteriorhodopsin at 4 °C and 20 °C.


  • Organizational Affiliation

    Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin
A, B
262Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: bopVNG_1467G
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYR
Query on LYR
A, B
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.05α = 90
b = 107.05β = 90
c = 149.86γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction

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 StatesP50 GM073197
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM098538
Ministry of Education and Science of the Russian FederationRussian FederationRFMEFI58716X0026

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.2: 2018-01-17
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description