8DCR | pdb_00008dcr

Cryo-EM structure of dobutamine-bound beta1-adrenergic receptor in complex with heterotrimeric Gs-protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structures of beta 1 -adrenergic receptor in complex with Gs and ligands of different efficacies.

Su, M.Paknejad, N.Zhu, L.Wang, J.Do, H.N.Miao, Y.Liu, W.Hite, R.K.Huang, X.Y.

(2022) Nat Commun 13: 4095-4095

  • DOI: https://doi.org/10.1038/s41467-022-31823-1
  • Primary Citation Related Structures: 
    8DCR, 8DCS

  • PubMed Abstract: 

    G-protein-coupled receptors (GPCRs) receive signals from ligands with different efficacies, and transduce to heterotrimeric G-proteins to generate different degrees of physiological responses. Previous studies revealed how ligands with different efficacies activate GPCRs. Here, we investigate how a GPCR activates G-proteins upon binding ligands with different efficacies. We report the cryo-EM structures of β 1 -adrenergic receptor (β 1 -AR) in complex with Gs (Gα s 1 2 ) and a partial agonist or a very weak partial agonist, and compare them to the β 1 -AR-Gs structure in complex with a full agonist. Analyses reveal similar overall complex architecture, with local conformational differences. Cellular functional studies with mutations of β 1 -AR residues show effects on the cellular signaling from β 1 -AR to the cAMP response initiated by the three different ligands, with residue-specific functional differences. Biochemical investigations uncover that the intermediate state complex comprising β 1 -AR and nucleotide-free Gs is more stable when binding a full agonist than a partial agonist. Molecular dynamics simulations support the local conformational flexibilities and different stabilities among the three complexes. These data provide insights into the ligand efficacy in the activation of GPCRs and G-proteins.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 163.37 kDa 
  • Atom Count: 7,934 
  • Modeled Residue Count: 1,000 
  • Deposited Residue Count: 1,442 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1A [auth B]339Bos taurusMutation(s): 0 
Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus)
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UniProt GroupP62871
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 35B [auth N]140Lama glamaMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortC [auth A]384Bos taurusMutation(s): 0 
Gene Names: GNASGNAS1
EC: 3.6.5
Membrane Entity: Yes 
UniProt
Find proteins for P04896 (Bos taurus)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Bos taurusMutation(s): 1 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Endolysin,Endolysin,Beta-1 adrenergic receptor chimeraE [auth R]508Meleagris gallopavoMutation(s): 0 
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
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Find proteins for P07700 (Meleagris gallopavo)
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UniProt GroupsP07700P00720
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y00
(Subject of Investigation/LOI)

Query on Y00



Download:Ideal Coordinates CCD File
F [auth R]DOBUTAMINE
C18 H23 N O3
JRWZLRBJNMZMFE-CYBMUJFWSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM138676

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary