7YFC

Cryo-EM structure of the histamine-bound histamine H4 receptor and Gq complex

• PDB DOI: https://doi.org/10.2210/pdb7YFC/pdb
• EM Map EMD-33785: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus, Lama glama
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2022-07-08 Released: 2023-10-25 
• Deposition Author(s): Im, D., Iwata, S., Asada, H.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the agonists binding and receptor selectivity of human histamine H4 receptor.

Im, D., Kishikawa, J.I., Shiimura, Y., Hisano, H., Ito, A., Fujita-Fujiharu, Y., Sugita, Y., Noda, T., Kato, T., Asada, H., Iwata, S.

(2023) Nat Commun 14: 6538

• DOI: https://doi.org/10.1038/s41467-023-42260-z

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 196.3 kDa 
• Atom Count: 9,882 
• Modelled Residue Count: 1,262 
• Deposited Residue Count: 1,756 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered G-alpha-q	A	361	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955
Find proteins for P63092 (Homo sapiens) Explore P63092  Go to UniProtKB:  P63092
PHAROS:  P63092 GTEx:  ENSG00000087460
UniProt Groups	P63096P63092

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	388	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
scFv16	C	259	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D [auth G]	71	Homo sapiens	Mutation(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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb35	E [auth N]	129	Lama glama	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histamine H4 receptor	F [auth R]	548	Homo sapiens	Mutation(s): 0  Gene Names: HRH4, GPCR105 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3N8 (Homo sapiens) Explore Q9H3N8  Go to UniProtKB:  Q9H3N8
PHAROS:  Q9H3N8 GTEx:  ENSG00000134489

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	H [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
HSM (Subject of Investigation/LOI)	G [auth R]	HISTAMINE C5 H9 N3 NTYJJOPFIAHURM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Im, D., Iwata, S., Asada, H.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101079

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2023-11-22
  Changes: Database references