6GDG

Cryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.11 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

Cryo-EM structure of the adenosine A2Areceptor coupled to an engineered heterotrimeric G protein.

Garcia-Nafria, J., Lee, Y., Bai, X., Carpenter, B., Tate, C.G.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.35946
  • Primary Citation of Related Structures:  
    6GDG

  • PubMed Abstract: 

    • The adenosine A 2A receptor (A 2A R) is a prototypical G protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G S . Here, we determine the structure by electron cryo-microscopy (cryo-EM) of A 2A R at pH 7 ...

    The adenosine A 2A receptor (A 2A R) is a prototypical G protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein G S . Here, we determine the structure by electron cryo-microscopy (cryo-EM) of A 2A R at pH 7.5 bound to the small molecule agonist NECA and coupled to an engineered heterotrimeric G protein, which contains mini-G S , the βγ subunits and nanobody Nb35. Most regions of the complex have a resolution of ~3.8 Å or better. Comparison with the 3.4 Å resolution crystal structure shows that the receptor and mini-G S are virtually identical and that the density of the side chains and ligand are of comparable quality. However, the cryo-EM density map also indicates regions that are flexible in comparison to the crystal structures, which unexpectedly includes regions in the ligand binding pocket. In addition, an interaction between intracellular loop 1 of the receptor and the β subunit of the G protein was observed.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TrxA,Adenosine receptor A2aA479Escherichia coli, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: trxA, ADORA2A, ADORA2
Membrane Entity: Yes 
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Find proteins for P0AA25 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AA25
Find proteins for P29274 (Homo sapiens)
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PHAROS:  P29274
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UniProt GroupsP0AA25P29274
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B339Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
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UniProt GroupP62873
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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PHAROS:  P59768
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UniProt GroupP59768
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortD248Homo sapiensMutation(s): 0 
Gene Names: GNAS, GNAS1, GSP
Membrane Entity: Yes 
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Find proteins for P63092 (Homo sapiens)
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PHAROS:  P63092
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UniProt GroupP63092
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
nanobody Nb35E156Lama glamaMutation(s): 0 
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Protein Feature View
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEC
Query on NEC
Download Ideal Coordinates CCD File 
F [auth A]N-ETHYL-5'-CARBOXAMIDO ADENOSINE
C12 H16 N6 O4
JADDQZYHOWSFJD-FLNNQWSLSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NEC BindingDB:  6GDG Ki: min: 1, max: 1.00e+4 (nM) from 39 assay(s)
IC50: min: 3.7, max: 366 (nM) from 8 assay(s)
EC50: min: 2.5, max: 394 (nM) from 15 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTREFMAC5

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomEMPSI 339995
Medical Research Council (United Kingdom)United KingdomMRC U105197215

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Other