6JZH

Structure of human A2A adenosine receptor in complex with ZM241385 obtained from SFX experiments under atmospheric pressure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure.

Shimazu, Y.Tono, K.Tanaka, T.Yamanaka, Y.Nakane, T.Mori, C.Terakado Kimura, K.Fujiwara, T.Sugahara, M.Tanaka, R.Doak, R.B.Shimamura, T.Iwata, S.Nango, E.Yabashi, M.

(2019) J Appl Crystallogr 52: 1280-1288

  • DOI: 10.1107/S1600576719012846
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a ...

    A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A 2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump-probe techniques.


    Organizational Affiliation

    RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
A
447Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: ADORA2A
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Go to UniProtKB:  P29274
NIH Common Fund Data Resources
PHAROS  P29274
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
ZMA
Query on ZMA

Download CCD File 
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
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZMAKi:  0.800000011920929   nM  BindingDB
ZMAKi:  1.399999976158142   nM  BindingDB
ZMAIC50:  33   nM  BindingDB
ZMAKi:  64   nM  BindingDB
ZMAKi:  0.9300000071525574   nM  BindingDB
ZMAIC50:  0.6800000071525574   nM  BindingDB
ZMAIC50:  1.5   nM  BindingDB
ZMAKi:  0.10000000149011612   nM  BindingDB
ZMAKi:  1.600000023841858   nM  BindingDB
ZMAKi:  5.300000190734863   nM  BindingDB
ZMAKi:  0.30000001192092896   nM  BindingDB
ZMAKi:  1.2000000476837158   nM  BindingDB
ZMAKi:  0.9100000262260437   nM  BindingDB
ZMAKi:  1.899999976158142   nM  BindingDB
ZMAKd:  0.2199999988079071   nM  BindingDB
ZMAKi:  2   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.17α = 90
b = 179.59β = 90
c = 142.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanBasis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanX-ray Free-Electron Laser Priority Strategy Program

Revision History 

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references