8IW4 | pdb_00008iw4

Cryo-EM structure of the SPE-bound mTAAR9-Gs complex


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8IW4

This is version 1.3 of the entry. See complete history

Literature

Structural basis of amine odorant perception by a mammal olfactory receptor.

Guo, L.Cheng, J.Lian, S.Liu, Q.Lu, Y.Zheng, Y.Zhu, K.Zhang, M.Kong, Y.Zhang, C.Rong, N.Zhuang, Y.Fang, G.Jiang, J.Zhang, T.Han, X.Liu, Z.Xia, M.Liu, S.Zhang, L.Liberles, S.D.Yu, X.Xu, Y.Yang, F.Li, Q.Sun, J.P.

(2023) Nature 618: 193-200

  • DOI: https://doi.org/10.1038/s41586-023-06106-4
  • Primary Citation Related Structures: 
    8ITF, 8IW1, 8IW4, 8IW7, 8IW9, 8IWE, 8IWM

  • PubMed Abstract: 

    Odorants are detected as smell in the nasal epithelium of mammals by two G-protein-coupled receptor families, the odorant receptors and the trace amine-associated receptors 1,2 (TAARs). TAARs emerged following the divergence of jawed and jawless fish, and comprise a large monophyletic family of receptors that recognize volatile amine odorants to elicit both intraspecific and interspecific innate behaviours such as attraction and aversion 3-5 . Here we report cryo-electron microscopy structures of mouse TAAR9 (mTAAR9) and mTAAR9-G s or mTAAR9-G olf trimers in complex with β-phenylethylamine, N,N-dimethylcyclohexylamine or spermidine. The mTAAR9 structures contain a deep and tight ligand-binding pocket decorated with a conserved D 3.32 W 6.48 Y 7.43 motif, which is essential for amine odorant recognition. In the mTAAR9 structure, a unique disulfide bond connecting the N terminus to ECL2 is required for agonist-induced receptor activation. We identify key structural motifs of TAAR family members for detecting monoamines and polyamines and the shared sequence of different TAAR members that are responsible for recognition of the same odour chemical. We elucidate the molecular basis of mTAAR9 coupling to G s and G olf by structural characterization and mutational analysis. Collectively, our results provide a structural basis for odorant detection, receptor activation and G olf coupling of an amine olfactory receptor.


  • Organizational Affiliation
    • Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China.

Macromolecule Content 

  • Total Structure Weight: 159.01 kDa 
  • Atom Count: 7,900 
  • Modeled Residue Count: 1,045 
  • Deposited Residue Count: 1,431 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short362Homo sapiensMutation(s): 0 
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 
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63096P63092
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-1377Homo 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
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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-259Homo 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
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Trace amine-associated receptor 9D [auth R]348Mus musculusMutation(s): 0 
Gene Names: Taar9
Membrane Entity: Yes 
UniProt
Find proteins for Q5QD04 (Mus musculus)
Explore Q5QD04 
Go to UniProtKB:  Q5QD04
Entity Groups
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UniProt GroupQ5QD04
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16E [auth S]285synthetic constructMutation(s): 0 

Small Molecules

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

Query on SPD



Download:Ideal Coordinates CCD File
F [auth R]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2018YFC1003600

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary