8HOC | pdb_00008hoc

Cryo-EM structure of ligand histamine-bound Histamine H4 receptor Gi complex

• PDB DOI: https://doi.org/10.2210/pdb8HOC/pdb
• EM Map EMD-34925: EMDB EMDataResource

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


• Deposited: 2022-12-09 Released: 2023-12-20 
• Deposition Author(s): Tang, W.Q., Sun, X.Y., Li, F.H., Wang, J.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Literature

Structure insights into Histamine H4 receptor activation by an endogenous ligand histamine and agonist imetit

Sun, X.Y., Li, F.H., Wang, J.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 180.49 kDa 
• Atom Count: 8,918 
• Modeled Residue Count: 1,127 
• Deposited Residue Count: 1,611 
• 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): 0  Gene Names: GNAI1 EC: 3.6.5 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	340	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 [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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562, Histamine H4 receptor fusion	D [auth R]	549	Homo sapiens	Mutation(s): 0  Gene Names: cybC, HRH4, GPCR105 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q9H3N8 (Homo sapiens) Explore Q9H3N8  Go to UniProtKB:  Q9H3N8
PHAROS:  Q9H3N8 GTEx:  ENSG00000134489
UniProt Groups	P0ABE7Q9H3N8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-chain variable fragment scFv16	E [auth S]	297	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ITF (Subject of Investigation/LOI)	F [auth R]	2-(1~{H}-imidazol-5-yl)ethyl carbamimidothioate C6 H10 N4 S PEHSVUKQDJULKE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ITF	BindingDB:  8HOC	Ki: min: 1.6, max: 3795.6 (nM) from 6 assay(s)
		EC50: min: 12.59, max: 51 (nM) from 2 assay(s)

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: 2023-12-20 
Deposition Author(s): Tang, W.Q., Sun, X.Y., Li, F.H., Wang, J.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary