8HDP | pdb_00008hdp

Structure of A2BR bound to endogenous agonists adenosine

• PDB DOI: https://doi.org/10.2210/pdb8HDP/pdb
• EM Map EMD-34677: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Camelus bactrianus
• Expression System: Spodoptera frugiperda, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-11-05 Released: 2023-01-18 
• Deposition Author(s): Cai, H., Xu, Y., Xu, H.E., Jiang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of adenosine receptor A 2B R bound to endogenous and synthetic agonists.

Cai, H., Xu, Y., Guo, S., He, X., Sun, J., Li, X., Li, C., Yin, W., Cheng, X., Jiang, H., Xu, H.E., Xie, X., Jiang, Y.

(2022) Cell Discov 8: 140-140

• PubMed: 36575181 
• DOI: https://doi.org/10.1038/s41421-022-00503-1
• Primary Citation of Related Structures:  
  8HDO, 8HDP

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Organizational Affiliation: 
• CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Lingang Laboratory, Shanghai, China.
CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Lingang Laboratory, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 126.88 kDa 
• Atom Count: 8,282 
• Modeled Residue Count: 1,041 
• Deposited Residue Count: 1,122 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric miniGs	A	246	Homo sapiens	Mutation(s): 0  Gene Names: GNAS, GNAS1, GSP 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	345	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 35	D [auth N]	128	Camelus bactrianus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine A2b receptor	E [auth R]	332	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P29275 (Homo sapiens) Explore P29275  Go to UniProtKB:  P29275
PHAROS:  P29275 GTEx:  ENSG00000170425

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	G [auth R], H [auth R], I [auth R], J [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
ADN	F [auth R]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADN	BindingDB:  8HDP	Ki: min: 5, max: 37 (nM) from 2 assay(s)
		EC50: min: 51, max: 5.13e+4 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Cai, H., Xu, Y., Xu, H.E., Jiang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81902085

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary