4HYX | pdb_00004hyx

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 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4HYX

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1073/pnas.1221442110
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 59.08 kDa 
  • Atom Count: 3,754 
  • Modeled Residue Count: 457 
  • Deposited Residue Count: 524 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacteriorhodopsin
A, B
262Halobacterium 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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / 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
C14

Query on C14



Download:Ideal Coordinates CCD File
O [auth B]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
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
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
GOL

Query on GOL



Download:Ideal Coordinates CCD File
S [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HEX

Query on HEX



Download:Ideal Coordinates CCD File
N [auth B]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
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

View Full Validation Report



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
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary