8RQQ

In meso structure of the adenosine A2a G protein-coupled receptor, A2aR, in 7.10 monoacylglycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins.

Krawinski, P.Smithers, L.van Dalsen, L.Boland, C.Ostrovitsa, N.Perez, J.Caffrey, M.

(2024) Cryst Growth Des 24: 2985-3001

  • DOI: https://doi.org/10.1021/acs.cgd.4c00087
  • Primary Citation of Related Structures:  
    8RQP, 8RQQ, 8RQR

  • PubMed Abstract: 

    A novel monoacylglycerol, 7.10 MAG, has been produced for use in the in meso (lipid cubic phase) crystallization of membrane proteins and complexes. 7.10 MAG differs from monoolein, the most extensively used lipid for in meso crystallization, in that it is shorter in chain length by one methylene and its cis olefinic bond is two carbons closer to the glycerol headgroup. These changes in structure alter the phase behavior of the hydrated lipid and the microstructure of the corresponding mesophases formed. Temperature-composition phase diagrams for 7.10 MAG have been constructed using small- and wide-angle X-ray scattering over a range of temperatures and hydration levels that span those used for crystallization. The phase diagrams include lamellar crystalline, fluid isotropic, lamellar liquid-crystalline, cubic- Ia 3 d, and cubic- Pn 3 m phases, as observed with monoolein. Conspicuous by its absence is the inverted hexagonal phase which is rationalized on the basis of 7.10 MAG's chemical constitution. The cubic phase prepared with the new lipid facilitates the growth of crystals that were used to generate high-resolution structures of intramembrane β-barrel and α-helical proteins. Compatibility of fully hydrated 7.10 MAG with cholesterol and phosphatidylcholine means that these two lipids can be used as additives to optimize crystallogenesis in screening trials with 7.10 MAG as the host lipid.


  • Organizational Affiliation

    Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine receptor A2a,Soluble cytochrome b562447Homo sapiensMutation(s): 3 
Gene Names: ADORA2AADORA2cybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P29274
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
A1H52
Query on A1H52

Download Ideal Coordinates CCD File 
K [auth A]7.10 monoacylglycerol (R-form)
C20 H38 O4
XTALOCBNHVPVKU-GNISGLHKSA-N
A1H2K (Subject of Investigation/LOI)
Query on A1H2K

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A],
P [auth A]
7.10 monoacylglycerol (S-form)
C20 H38 O4
XTALOCBNHVPVKU-VYENPZKTSA-N
ZMA
Query on ZMA

Download Ideal Coordinates CCD File 
B [auth A]4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol
C16 H15 N7 O2
PWTBZOIUWZOPFT-UHFFFAOYSA-N
GOL
Query on GOL

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N [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

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Q [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.69α = 90
b = 180.44β = 90
c = 141.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland16/IA/4435
Science Foundation IrelandIreland22/FFP-A/10278
Irish Research CouncilIrelandGOIPG/2019/3074
Irish Research CouncilIrelandGOIPD/2021/40

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references