9BHL | pdb_00009bhl

Human proton sensing receptor GPR65 in complex with miniGs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9BHL

This is version 1.2 of the entry. See complete history

Literature

Molecular basis of proton sensing by G protein-coupled receptors.

Howard, M.K.Hoppe, N.Huang, X.P.Mitrovic, D.Billesbolle, C.B.Macdonald, C.B.Mehrotra, E.Rockefeller Grimes, P.Trinidad, D.D.Delemotte, L.English, J.G.Coyote-Maestas, W.Manglik, A.

(2025) Cell 188: 671

  • DOI: https://doi.org/10.1016/j.cell.2024.11.036
  • Primary Citation Related Structures: 
    9BHL, 9BHM, 9BI6, 9BIP

  • PubMed Abstract: 

    Three proton-sensing G protein-coupled receptors (GPCRs)-GPR4, GPR65, and GPR68-respond to extracellular pH to regulate diverse physiology. How protons activate these receptors is poorly understood. We determined cryogenic-electron microscopy (cryo-EM) structures of each receptor to understand the spatial arrangement of proton-sensing residues. Using deep mutational scanning (DMS), we determined the functional importance of every residue in GPR68 activation by generating ∼9,500 mutants and measuring their effects on signaling and surface expression. Constant-pH molecular dynamics simulations provided insights into the conformational landscape and protonation patterns of key residues. This unbiased approach revealed that, unlike other proton-sensitive channels and receptors, no single site is critical for proton recognition. Instead, a network of titratable residues extends from the extracellular surface to the transmembrane region, converging on canonical motifs to activate proton-sensing GPCRs. Our approach integrating structure, simulations, and unbiased functional interrogation provides a framework for understanding GPCR signaling complexity.


  • Organizational Affiliation
    • Tetrad graduate program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA.

Macromolecule Content 

  • Total Structure Weight: 127.02 kDa 
  • Atom Count: 7,716 
  • Modeled Residue Count: 969 
  • Deposited Residue Count: 1,121 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short261Homo sapiensMutation(s): 6 
Gene Names: GNASGNAS1GSP
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63092
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1370Homo 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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 35C [auth N]142Lama glamaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Psychosine receptorD [auth R]348Homo sapiensMutation(s): 0 
Gene Names: GPR65TDAG8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYL9 (Homo sapiens)
Explore Q8IYL9 
Go to UniProtKB:  Q8IYL9
PHAROS:  Q8IYL9
GTEx:  ENSG00000140030 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IYL9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chan Zuckerberg InitiativeUnited States--
Howard Hughes Medical Institute (HHMI)United States--
The Vallee Foundation Inc.United States--
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM139786
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesF31HL164045

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-21
    Changes: Data collection