8HDO | pdb_00008hdo

Structure of A2BR bound to synthetic agonists BAY 60-6583

PDB DOI: https://doi.org/10.2210/pdb8HDO/pdb
EM Map EMD-34676: 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 OPM PDBTM MemProtMD mpstruc

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00503-1
Primary Citation Related Structures:
8HDO, 8HDP

Organizational Affiliation

CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content

Total Structure Weight: 128.16 kDa
Atom Count: 8,277
Modeled Residue Count: 1,028
Deposited Residue Count: 1,122
Unique protein chains: 5

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63092
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 35	D [auth N]	128	Camelus bactrianus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29275
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain J [auth R] SDF format, chain K [auth R] SDF format, chain L [auth R] SDF format, chain I [auth R] SDF format, chain H [auth R] SDF format, chain G [auth R] SDF format, chain F [auth R] MOL2 format, chain J [auth R] MOL2 format, chain K [auth R] MOL2 format, chain L [auth R] MOL2 format, chain I [auth R] MOL2 format, chain H [auth R] MOL2 format, chain G [auth R] MOL2 format, chain F [auth R] mmCIF format, chain J [auth R] mmCIF format, chain K [auth R] mmCIF format, chain L [auth R] mmCIF format, chain I [auth R] mmCIF format, chain H [auth R] mmCIF format, chain G [auth R] mmCIF format, chain F [auth R]	F [auth R] G [auth R] H [auth R] I [auth R] J [auth R] F [auth R], G [auth R], H [auth R], I [auth R], J [auth R], K [auth R], L [auth R]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain F [auth R] Focus chain G [auth R] Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Focus chain K [auth R] Focus chain L [auth R] Interactions & Density Focus chain F [auth R] Focus chain G [auth R] Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Focus chain K [auth R] Focus chain L [auth R]
I5D (Subject of Investigation/LOI) Query on I5D Download:Ideal Coordinates CCD File SDF format, chain M [auth R] MOL2 format, chain M [auth R] mmCIF format, chain M [auth R]	M [auth R]	2-[6-azanyl-3,5-dicyano-4-[4-(cyclopropylmethoxy)phenyl]pyridin-2-yl]sulfanylethanamide C₁₉ H₁₇ N₅ O₂ S ZTYHZMAZUWOXNC-UHFFFAOYSA-N		Interactions Focus chain M [auth R] Interactions & Density Focus chain M [auth R]