4HYX

Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-4 DMPC Bicelle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins.

Lee, S.C.Bennett, B.C.Hong, W.X.Fu, Y.Baker, K.A.Marcoux, J.Robinson, C.V.Ward, A.B.Halpert, J.R.Stevens, R.C.Stout, C.D.Yeager, M.J.Zhang, Q.

(2013) Proc Natl Acad Sci U S A 110: E1203-E1211

  • DOI: 10.1073/pnas.1221442110
  • Primary Citation of Related Structures:  
    4HWL, 4HYX

  • PubMed Abstract: 
  • Amphiphile selection is a critical step for structural studies of membrane proteins (MPs). We have developed a family of steroid-based facial amphiphiles (FAs) that are structurally distinct from conventional detergents and previously developed FAs. The unique FAs stabilize MPs and form relatively small protein-detergent complexes (PDCs), a property considered favorable for MP crystallization ...

    Amphiphile selection is a critical step for structural studies of membrane proteins (MPs). We have developed a family of steroid-based facial amphiphiles (FAs) that are structurally distinct from conventional detergents and previously developed FAs. The unique FAs stabilize MPs and form relatively small protein-detergent complexes (PDCs), a property considered favorable for MP crystallization. We attempted to crystallize several MPs belonging to different protein families, including the human gap junction channel protein connexin 26, the ATP binding cassette transporter MsbA, the seven-transmembrane G protein-coupled receptor-like bacteriorhodopsin, and cytochrome P450s (peripheral MPs). Using FAs alone or mixed with other detergents or lipids, we obtained 3D crystals of the above proteins suitable for X-ray crystallographic analysis. The fact that FAs enhance MP crystallizability compared with traditional detergents can be attributed to several properties, including increased protein stability, formation of small PDCs, decreased PDC surface flexibility, and potential to mediate crystal lattice contacts.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BacteriorhodopsinA, B262Halobacterium salinarumMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
C14
Query on C14

Download Ideal Coordinates CCD File 
O [auth B]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
R [auth B]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

Download Ideal Coordinates CCD File 
D [auth A],
J [auth A],
P [auth B],
Q [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
S [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

Download Ideal Coordinates CCD File 
N [auth B]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.89α = 90
b = 112.92β = 113.83
c = 56.29γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references