6LPK

A2AR crystallized in EROCOC17+4, LCP-SFX at 293 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.

Ihara, K.Hato, M.Nakane, T.Yamashita, K.Kimura-Someya, T.Hosaka, T.Ishizuka-Katsura, Y.Tanaka, R.Tanaka, T.Sugahara, M.Hirata, K.Yamamoto, M.Nureki, O.Tono, K.Nango, E.Iwata, S.Shirouzu, M.

(2020) Sci Rep 10: 19305-19305

  • DOI: https://doi.org/10.1038/s41598-020-76277-x
  • Primary Citation of Related Structures:  
    6LPJ, 6LPK, 6LPL

  • PubMed Abstract: 

    In meso crystallization of membrane proteins relies on the use of lipids capable of forming a lipidic cubic phase (LCP). However, almost all previous crystallization trials have used monoacylglycerols, with 1-(cis-9-octadecanoyl)-rac-glycerol (MO) being the most widely used lipid. We now report that EROCOC 17+4 mixed with 10% (w/w) cholesterol (Fig. 1) serves as a new matrix for crystallization and a crystal delivery medium in the serial femtosecond crystallography of Adenosine A 2A receptor (A 2A R). The structures of EROCOC 17+4 -matrix grown A 2A R crystals were determined at 2.0 Å resolution by serial synchrotron rotation crystallography at a cryogenic temperature, and at 1.8 Å by LCP-serial femtosecond crystallography, using an X-ray free-electron laser at 4 and 20 °C sample temperatures, and are comparable to the structure of the MO-matrix grown A 2A R crystal (PDB ID: 4EIY). Moreover, X-ray scattering measurements indicated that the EROCOC 17+4 /water system did not form the crystalline L C phase at least down to - 20 °C, in marked contrast to the equilibrium MO/water system, which transforms into the crystalline L C phase below about 17 °C. As the L C phase formation within the LCP-matrix causes difficulties in protein crystallography experiments in meso, this feature of EROCOC 17+4 will expand the utility of the in meso method.


  • Organizational Affiliation

    RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a447Homo sapiensEscherichia coliMutation(s): 3 
Gene Names: ADORA2AADORA2cybC
Membrane Entity: Yes 
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
GTEx:  ENSG00000128271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P29274
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ER0 (Subject of Investigation/LOI)
Query on ER0

Download Ideal Coordinates CCD File 
Q [auth A],
X [auth A]
[(2~{R},3~{S})-2,3,4-tris(oxidanyl)butyl] (5~{R},9~{R},13~{R})-5,9,13,17-tetramethyloctadecanoate
C26 H52 O5
RSTFOCYJXCUQHZ-UUFXTFJOSA-N
CLR
Query on CLR

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D [auth A],
E [auth A],
F [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
ZMA
Query on ZMA

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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
8K6
Query on 8K6

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K [auth A],
S [auth A],
T [auth A]
Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
MYS
Query on MYS

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AA [auth A]
H [auth A]
J [auth A]
O [auth A]
R [auth A]
AA [auth A],
H [auth A],
J [auth A],
O [auth A],
R [auth A],
Y [auth A]
PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
TRD
Query on TRD

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BA [auth A],
U [auth A],
W [auth A],
Z [auth A]
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
D12
Query on D12

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G [auth A]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
UND
Query on UND

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P [auth A]UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
D10
Query on D10

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L [auth A]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT
Query on OCT

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M [auth A],
N [auth A],
V [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX
Query on HEX

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I [auth A]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
NA
Query on NA

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

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.5α = 90
b = 179.2β = 90
c = 142.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP16K14688

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description