8HTI

Human Consensus Olfactory Receptor OR52c in Complex with Octanoic Acid (OCA) and G Protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 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

Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family.

Choi, C.Bae, J.Kim, S.Lee, S.Kang, H.Kim, J.Bang, I.Kim, K.Huh, W.K.Seok, C.Park, H.Im, W.Choi, H.J.

(2023) Nat Commun 14: 8105-8105

  • DOI: https://doi.org/10.1038/s41467-023-43983-9
  • Primary Citation of Related Structures:  
    8HTG, 8HTI, 8J46, 8W77

  • PubMed Abstract: 

    Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52 cs ), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52 cs reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52 cs demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.


  • Organizational Affiliation

    Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short393Homo sapiensMutation(s): 1 
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1357Homo 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 
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UniProt GroupP62873
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  • Reference Sequence
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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 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 35D [auth N]138Lama glamaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Consensus Olfactory Receptor OR52cE [auth R]323Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OCA (Subject of Investigation/LOI)
Query on OCA

Download Ideal Coordinates CCD File 
F [auth R]OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Samsung Science and Technology FoundationKorea, Republic OfSSTF-BA1901-09

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary