8GFY

CryoEM structure of beta-2-adrenergic receptor in complex with GTP-bound Gs heterotrimer (transition intermediate #4 of 20)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Time-resolved cryo-EM of G-protein activation by a GPCR.

Papasergi-Scott, M.M.Perez-Hernandez, G.Batebi, H.Gao, Y.Eskici, G.Seven, A.B.Panova, O.Hilger, D.Casiraghi, M.He, F.Maul, L.Gmeiner, P.Kobilka, B.K.Hildebrand, P.W.Skiniotis, G.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07153-1
  • Primary Citation of Related Structures:  
    8GDZ, 8GE1, 8GE2, 8GE3, 8GE4, 8GE5, 8GE6, 8GE7, 8GE8, 8GE9, 8GEA, 8GEB, 8GEC, 8GED, 8GEE, 8GEF, 8GEG, 8GEH, 8GEI, 8GEJ, 8GFV, 8GFW, 8GFX, 8GFY, 8GFZ, 8GG0, 8GG1, 8GG2, 8GG3, 8GG4, 8GG5, 8GG6, 8GG7, 8GG8, 8GG9, 8GGA, 8GGB, 8GGC, 8GGE, 8GGF, 8GGI, 8GGJ, 8GGK, 8GGL, 8GGM, 8GGN, 8GGO, 8GGP, 8GGQ, 8GGR

  • PubMed Abstract: 

    G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating guanine nucleotide exchange in the Gα subunit 1 . To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G-protein complex. By monitoring the transitions of the stimulatory G s protein in complex with the β 2 -adrenergic receptor at short sequential time points after GTP addition, we identified the conformational trajectory underlying G-protein activation and functional dissociation from the receptor. Twenty structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of main events driving G-protein activation in response to GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to Gα switch regions and the α5 helix that weaken the G-protein-receptor interface. Molecular dynamics simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP on closure of the α-helical domain against the nucleotide-bound Ras-homology domain correlates with α5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signalling events.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short380Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63092
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1343Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59768
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2 adrenergic receptorD [auth R]460Homo sapiensMutation(s): 2 
Gene Names: ADRB2ADRB2RB2AR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
PHAROS:  P07550
GTEx:  ENSG00000169252 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07550
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
G1I
Query on G1I

Download Ideal Coordinates CCD File 
F [auth R](5R,6R)-6-(methylamino)-5,6,7,8-tetrahydronaphthalene-1,2,5-triol
C11 H15 N O3
VJBMHARWYAGTQQ-PSASIEDQSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references