5ITE

2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Octylglucoside (OG) Detergent Micelles


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.str.2016.12.004
  • Primary Citation of Related Structures:  
    5ITC, 5ITE

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin-I
A, B, C
268Haloquadratum walsbyi DSM 16790Mutation(s): 0 
Gene Names: bop1bopIHQ_1014A
Membrane Entity: Yes 
UniProt
Find proteins for Q18DH8 (Haloquadratum walsbyi (strain DSM 16790 / HBSQ001))
Explore Q18DH8 
Go to UniProtKB:  Q18DH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18DH8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
I [auth B]
J [auth B]
M [auth C]
F [auth A],
H [auth B],
I [auth B],
J [auth B],
M [auth C],
N [auth C]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLB
Query on OLB

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
O [auth C]
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
L [auth C]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.442α = 90
b = 61.565β = 116.8
c = 119.689γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description