8WDT | pdb_00008wdt

Crystal structure of the human adenosine A2A receptor in complex with photoresponsive ligand photoNECA(blue)

• PDB DOI: https://doi.org/10.2210/pdb8WDT/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2023-09-16 Released: 2024-01-17 
• Deposition Author(s): Araya, T., Asada, H., Iwata, S., Im, D.H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.34 Å
• R-Value Free: 
  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Models: experimental

Literature

Crystal structure reveals the binding mode and selectivity of a photoswitchable ligand for the adenosine A 2A receptor.

Araya, T., Matsuba, Y., Suzuki, H., Doura, T., Nuemket, N., Nango, E., Yamamoto, M., Im, D., Asada, H., Kiyonaka, S., Iwata, S.

(2023) Biochem Biophys Res Commun 695: 149393-149393

• PubMed: 38171234 
• DOI: https://doi.org/10.1016/j.bbrc.2023.149393
• Primary Citation Related Structures: 
  8WDT


• PubMed Abstract: 
  

  Rational synthetic expansion of photoresponsive ligands is important for photopharmacological studies. Adenosine A _2A receptor (A _2A R) is stimulated by adenosine and related in Parkinson's disease and other diseases. Here, we report the crystal structure of the A _2A R in complex with the novel photoresponsive ligand photoNECA (blue) at 3.34 Å resolution. PhotoNECA (blue) was designed for this structural study and the cell-based assay showed a photoresponsive and receptor selective characteristics of photoNECA (blue) for A _2A R. The crystal structure explains the binding mode, photoresponsive mechanism and receptor selectivity of photoNECA (blue). Our study would promote not only the rational design of photoresponsive ligands but also dynamic structural studies of A _2A R.

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Organizational Affiliation: 
• Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
RIKEN SPring-8 Center, Hyogo, 679-5148, Japan; JASRI, Hyogo, 679-5148, Japan.
RIKEN SPring-8 Center, Hyogo, 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan.
RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan. Electronic address: [e-mail].
Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan; Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, 464-8603, Japan. Electronic address: [e-mail].
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan; RIKEN SPring-8 Center, Hyogo, 679-5148, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 87.2 kDa 
• Atom Count: 5,667 
• Modeled Residue Count: 734 
• Deposited Residue Count: 788 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a	A	351	Homo sapiens	Mutation(s): 6  Gene Names: ADORA2A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P29274 (Homo sapiens) Explore P29274  Go to UniProtKB:  P29274
PHAROS:  P29274 GTEx:  ENSG00000128271

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab fragment light chain	B	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab fragment heavy chain	C	224	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WCH (Subject of Investigation/LOI)	D [auth A]	(2S,3S,4R,5R)-5-(6-amino-2-((E)-phenyldiazenyl)-9H-purin-9-yl)-N-ethyl-3,4-dihydroxytetrahydrofuran-2-carboxamide C18 H20 N8 O4 TWQRPAGBMNXURX-APJVYBOUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.34 Å
• R-Value Free:  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 372.64	α = 90
b = 52.52	β = 94.79
c = 63.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Araya, T., Asada, H., Iwata, S., Im, D.H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary