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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 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
PHAROS:  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]
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
Binding Affinity Annotations 
IDSourceBinding Affinity
ZMA BindingDB:  6LPK Ki: min: 0.1, max: 395 (nM) from 18 assay(s)
Kd: min: 0.22, max: 286 (nM) from 2 assay(s)
IC50: min: 0.68, max: 81 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.209 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 2 2 21
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ER0Click on this verticalbar to view details

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
  • Version 1.3: 2024-10-16
    Changes: Structure summary