5ITC

2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Styrene Maleic Acid (SMA) Polymer Nanodiscs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs.

Broecker, J.Eger, B.T.Ernst, O.P.

(2017) Structure 25: 384-392

  • DOI: 10.1016/j.str.2016.12.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For some membrane proteins, detergent-mediated solubilization compromises protein stability and functionality, often impairing biophysical and structural analyses. Hence, membrane-protein structure determination is a continuing bottleneck in the fiel ...

    For some membrane proteins, detergent-mediated solubilization compromises protein stability and functionality, often impairing biophysical and structural analyses. Hence, membrane-protein structure determination is a continuing bottleneck in the field of protein crystallography. Here, as an alternative to approaches mediated by conventional detergents, we report the crystallogenesis of a recombinantly produced membrane protein that never left a lipid bilayer environment. We used styrene-maleic acid (SMA) copolymers to solubilize lipid-embedded proteins into SMA nanodiscs, purified these discs by affinity and size-exclusion chromatography, and transferred proteins into the lipidic cubic phase (LCP) for in meso crystallization. The 2.0-Å structure of an α-helical seven-transmembrane microbial rhodopsin thus obtained is of high quality and virtually identical to the 2.2-Å structure obtained from traditional detergent-based purification and subsequent LCP crystallization.


    Organizational Affiliation

    Structural Neurobiology, Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada. Electronic address: jana.broecker@utoronto.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriorhodopsin-I
A, B, C
268Haloquadratum walsbyi (strain DSM 16790 / HBSQ001)Mutation(s): 0 
Gene Names: bop1 (bopI)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Bacteriorhodopsin (BR), trimer in asymmetric unit
Find proteins for Q18DH8 (Haloquadratum walsbyi (strain DSM 16790 / HBSQ001))
Go to UniProtKB:  Q18DH8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB

Download SDF File 
Download CCD File 
A, B, C
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
OLC
Query on OLC

Download SDF File 
Download CCD File 
A, C
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
RET
Query on RET

Download SDF File 
Download CCD File 
A, B, C
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.715α = 90.00
b = 61.586β = 116.16
c = 119.089γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Government of CanadaCanadaCanada Excellence Research Chair program
German Research Foundation (DFG)GermanyBR 5124/1-1

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references