8IRJ | pdb_00008irj

Cryo-EM structure of an orphan GPCR

• PDB DOI: https://doi.org/10.2210/pdb8IRJ/pdb
• EM Map EMD-35676: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-03-17 Released: 2024-09-18 
• Deposition Author(s): Yun, Y., Jeong, H., Lee, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human class C orphan GPCR GPR179 involved in visual processing.

Yun, Y., Jeong, H., Laboute, T., Martemyanov, K.A., Lee, H.H.

(2024) Nat Commun 15: 8299-8299

• PubMed: 39333506 
• DOI: https://doi.org/10.1038/s41467-024-52584-z
• Primary Citation Related Structures: 
  8IRJ


• PubMed Abstract: 
  

  GPR179, an orphan class C GPCR, is expressed at the dendritic tips of ON-bipolar cells in the retina. It plays a pivotal role in the initial synaptic transmission of visual signals from photoreceptors, and its deficiency is known to be the cause of complete congenital stationary night blindness. Here, we present the cryo-electron microscopy structure of human GPR179. Notably, the transmembrane domain (TMD) of GPR179 forms a homodimer through the TM1/7 interface with a single inter-protomer disulfide bond, adopting a noncanonical dimerization mode. Furthermore, the TMD dimer exhibits architecture well-suited for the highly curved membrane of the dendritic tip and distinct from the flat membrane arrangement observed in other class C GPCR dimers. Our structure reveals unique structural features of GPR179 TMD, setting it apart from other class C GPCRs. These findings provide a foundation for understanding signal transduction through GPR179 in visual processing and offers insights into the underlying causes of ocular diseases.

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Organizational Affiliation: 
• Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
Center for Research Equipment, Korea Basic Science Institute, Chungcheongbuk-do, 28119, Republic of Korea.
Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, 33458, USA.
Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France.
Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, 33458, USA. [e-mail].
Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 167.92 kDa 
• Atom Count: 8,228 
• Modeled Residue Count: 1,062 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable G-protein coupled receptor 179	A, B	759	Homo sapiens	Mutation(s): 0  Gene Names: GPR179, GPR158L, GPR158L1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PRD1 (Homo sapiens) Explore Q6PRD1  Go to UniProtKB:  Q6PRD1
PHAROS:  Q6PRD1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.49 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Yun, Y., Jeong, H., Lee, H.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection
• Version 1.3: 2025-10-01
  Changes: Data collection, Database references