7XY6

Adenosine receptor bound to an agonist in complex with G protein obtained by cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of the human adenosine A 2B receptor-G s signaling complex.

Chen, Y.Zhang, J.Weng, Y.Xu, Y.Lu, W.Liu, W.Liu, M.Hua, T.Song, G.

(2022) Sci Adv 8: eadd3709-eadd3709

  • DOI: https://doi.org/10.1126/sciadv.add3709
  • Primary Citation of Related Structures:  
    7XY6, 7XY7

  • PubMed Abstract: 

    The human adenosine A 2B receptor (A 2B R) is a class A G protein-coupled receptor that is involved in several major physiological and pathological processes throughout the body. A 2B R recognizes its ligands adenosine and NECA with relatively low affinity, but the detailed mechanism for its ligand recognition and signaling is still elusive. Here, we present two structures determined by cryo-electron microscopy of A 2B R bound to its agonists NECA and BAY60-6583, each coupled to an engineered G s protein. The structures reveal conserved orthosteric binding pockets with subtle differences, whereas the selectivity or specificity can mainly be attributed to regions extended from the orthosteric pocket. We also found that BAY60-6583 occupies a secondary pocket, where residues V250 6.51 and N273 7.36 were two key determinants for its selectivity against A 2B R. This study offers a better understanding of ligand selectivity for the adenosine receptor family and provides a structural template for further development of A 2B R ligands for related diseases.


  • Organizational Affiliation

    Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short243Homo sapiensMutation(s): 7 
Gene Names: GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1366Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]73Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Adenosine receptor A2b,LgBiTD [auth R]628Escherichia coliHomo sapiensOplophorus gracilirostris
This entity is chimeric
Mutation(s): 2 
Gene Names: cybCADORA2B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P29275 (Homo sapiens)
Explore P29275 
Go to UniProtKB:  P29275
PHAROS:  P29275
GTEx:  ENSG00000170425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P29275
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I5D (Subject of Investigation/LOI)
Query on I5D

Download Ideal Coordinates CCD File 
E [auth R]2-[6-azanyl-3,5-dicyano-4-[4-(cyclopropylmethoxy)phenyl]pyridin-2-yl]sulfanylethanamide
C19 H17 N5 O2 S
ZTYHZMAZUWOXNC-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I5D BindingDB:  7XY6 EC50: 31 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32022038
National Natural Science Foundation of China (NSFC)China31770898

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Source and taxonomy, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Source and taxonomy