8YN6

Cryo-EM structure of histamine H3 receptor in complex with imetit and Gi

• PDB DOI: https://doi.org/10.2210/pdb8YN6/pdb
• EM Map EMD-39416: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2024-03-10 Released: 2024-10-09 
• Deposition Author(s): Zhang, X., Liu, G., Li, X., Gong, W.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of ligand recognition and activation of the histamine receptor family

Zhang, X., Liu, G., Zhong, Y.N., Zhang, R., Yang, C.C., Niu, C., Pu, X., Sun, J., Zhang, T., Yang, L., Zhang, C., Li, X., Shen, X., Xiao, P., Sun, J.P., Gong, W.

(2024) Nat Commun 15: 8296

• DOI: https://doi.org/10.1038/s41467-024-52585-y

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 191.17 kDa 
• Atom Count: 8,942 
• Modelled Residue Count: 1,142 
• Deposited Residue Count: 1,715 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 4  Gene Names: GNAI1
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	376	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment scFv16	D [auth E]	255	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histamine H3 receptor	E [auth R]	659	Homo sapiens	Mutation(s): 0  Gene Names: HRH3, GPCR97
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5N1 (Homo sapiens) Explore Q9Y5N1  Go to UniProtKB:  Q9Y5N1
PHAROS:  Q9Y5N1 GTEx:  ENSG00000101180

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	G [auth R], H [auth R], I [auth R], J [auth R], K [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
ITF (Subject of Investigation/LOI)	F [auth R]	2-(1~{H}-imidazol-5-yl)ethyl carbamimidothioate C6 H10 N4 S PEHSVUKQDJULKE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Zhang, X., Liu, G., Li, X., Gong, W.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0904100
National Natural Science Foundation of China (NSFC)	China	T2221005

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release