9JG1: Histamine H4 receptor,Soluble cytochrome b562

Cryo-EM structure of Adriforant-bound Histamine receptor 4 H4R at inactive state. Determined by electron microscopy at 3.62 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 3.62 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 3
Atoms: 4,730
Mol. weight: 97.53 kDa
Ligands: A1EBW
Released: 3 Dec 2025

Explore 9JG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JG1 contains 21 α-helices and 22 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	11	1	2
β-strand	20-26	7	1
β-strand	34-39	6	2
β-strand	46-50	5	2
β-strand	54-55	2	2
α-helix	56	1
β-strand	63-68	6	1
β-strand	71-76	6	1
β-strand	86-91	6	2
α-helix	95-97	3
β-strand	99-100	2	2
β-strand	104-105	2	2

Chain L: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	3
β-strand	13-14	2	4
β-strand	21-26	6	3
β-strand	35-42	8	4
β-strand	48-54	7	4
β-strand	61-63	3	4
β-strand	71-76	6	3
β-strand	81-86	6	3
β-strand	95-103	9	4
α-helix	108-111	4
β-strand	115	1	4
β-strand	121-124	4	4

Chain R: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	12-42	31
α-helix	44-46	3
α-helix	49-52	4
α-helix	56-76	21
α-helix	84-116	33
α-helix	119-123	5
α-helix	126-128	3
α-helix	130-154	25
α-helix	172-179	8
α-helix	180-184	5
α-helix	185-400	46
α-helix	408-423	16
α-helix	438-463	26
α-helix	476-480	5
α-helix	485-527	43
α-helix	545-564	20
α-helix	565-567	3
α-helix	571-574	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histamine H4 receptor,Soluble cytochrome b562	R	protein	427	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), Q9H3N8 (AlphaFold model)
anti-BRIL Fab Heavy chain	H	protein	222	Homo sapiens
anti-BRIL Fab Light chain	L	protein	226	Homo sapiens

Sequence of entity 1 (R), FASTA

>9JG1_1 Histamine H4 receptor,Soluble cytochrome b562 (chains R)
MPDTNSTINLSLSTRVTLAFFMSLVAFAIMLGNALVILAFVVDKNLRHRSSYFFLNLAIS
DFFVGVISIPLYIPHTLFEWDFGKEICVFWLTTDYLLCTASVYNIVLISYDRYLSVSNAV
SYRTQHTGVLKIVTLMVAVWVLAFLVNGPMILVSESWKDEGSECEPGFFSEWYILAITSF
LEFVIPVILVAYFNMNIYWSLWKRDHLARRQLADLEDNWETLNDNLKVIEKADNAAQVKD
ALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQ
AAAEQLKTTRNAYIQKYLERARSTLQREHVELLRARRLAKSLAILLGVFAVCWAPYSLFT
IVLSFYSSATGPKSVWYRIAFWLQWFNSFVNPLLYPLCHKRFQKAFLKIFCIKKQPLPSQ
HSRSVSS

Sequence of entity 2 (H), FASTA

>9JG1_2 anti-BRIL Fab Heavy chain (chains H)
MSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGV
PSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFI
FPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGGHHHHHH

Sequence of entity 3 (L), FASTA

>9JG1_3 anti-BRIL Fab Light chain (chains L)
MSEVQLVESGGGLVQPGGSLRLSCAASGFNVVVFSIHWVRQAPGKGLEWVAYISSSSGST
SYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGT
LVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Ligands and cofactors

ID	Name	Formula	Copies
A1EBW	Adriforant	C13 H22 N6	1

Primary citation

Decoding ligand recognition and constitutive activation of histamine H3 and H4 receptors. Jin, S.S., Zhang, H., Yan, J.H. et al. Acta Pharmacol Sin (2026) 47:186-196. DOI 10.1038/s41401-025-01633-4 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

Browse structure collections

About this viewer

MolViewer shows 9JG1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.