9JEQ: PDB entry 9JEQ

Cryo-EM structure of Histamine-bound Histamine receptor 3 H3R G protein complex. Determined by electron microscopy at 3.05 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 3.05 Å
Organisms: Homo sapiens, Bos taurus, Mus musculus
Chains: 5
Atoms: 8,890
Mol. weight: 159.39 kDa
Ligands: HSM
Released: 24 Sept 2025

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

Secondary structure: helices and β-sheets

9JEQ contains 29 α-helices and 62 β-strands across 5 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 A: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-40	8	8
α-helix	47-53	7
β-strand	185-190	6	8
β-strand	195-200	6	8
α-helix	208-211	4
α-helix	213-215	3
β-strand	220-226	7	8
α-helix	227-229	3
β-strand	233	1	9
β-strand	241	1	9
α-helix	242-255	14
β-strand	263-269	7	8
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	8
α-helix	330-347	18
α-helix	348-350	3

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
β-strand	103-105	3	3
β-strand	111-114	4	3
β-strand	116	1	4
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	166-170	5	4
β-strand	175-180	6	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-222	5	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	249-254	6	6
β-strand	260-265	6	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	303-308	6	7
β-strand	317-320	4	1
β-strand	327-330	4	1
β-strand	336-339	4	1

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-23	18
α-helix	30-43	14

Chain R: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	34-61	28
α-helix	68-96	29
α-helix	106-137	32
α-helix	139-145	7
α-helix	149-178	30
α-helix	197-203	7
α-helix	204-208	5
α-helix	209-234	26
α-helix	348-383	36
α-helix	393-411	19
α-helix	418-423	6

Chain S: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	17-25	9	10
β-strand	33-39	7	12
β-strand	45-52	8	12
β-strand	56-60	5	12
β-strand	68-73	6	10
β-strand	78-84	7	10
β-strand	93-99	7	12
β-strand	110-111	2	12
β-strand	115	1	12
β-strand	118-119	2	11
β-strand	141	1	13
β-strand	146-147	2	12
α-helix	149-150	2
β-strand	155-160	6	13
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	12
β-strand	185-190	6	12
β-strand	194-195	2	12
α-helix	196	1
β-strand	205	1	13
β-strand	211-216	6	13
β-strand	225-231	7	12
β-strand	238-239	2	12
β-strand	243-245	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	58	Bos taurus	P63212 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	352	Homo sapiens	P63096 (AlphaFold model)
Histamine H3 receptor	R	protein	445	Homo sapiens	Q9Y5N1 (AlphaFold model)
ScFv16	S	protein	251	Mus musculus

Sequence of entity 1 (B), FASTA

>9JEQ_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (G), FASTA

>9JEQ_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 3 (A), FASTA

>9JEQ_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
CTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAGYS
EEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAE
LAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTT
GIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNR
MHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAY
IQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (R), FASTA

>9JEQ_4 Histamine H3 receptor (chains R)
MERAPPDGPLNASGALAGEAAAAGGARGFSAAWTAVLAALMALLIVATVLGNALVMLAFV
ADSSLRTQNNFFLLNLAISDFLVGAFCIPLYVPYVLTGRWTFGRGLCKLWLVVDYLLCTS
SAFNIVLISYDRFLSVTRAVSYRAQNGDTRRAVRKMLLVWVLAFLLYGPAILSWEYLSGG
SSIPEGHCYAEFFYNWYFLITASTLEFFTPFLSVTFFNLSIYLNIQRRTRLRLDGAREAA
GPEPPPEAQPSPPPPPGCWGCWQKGHGEAMPLHRYGVGEAAVGAEAGEATLGGGGGGGSV
ASPTSSSGSSSRGTERPRSLKRGSKPSASSASLEKRMKMVSQSFTQRFRLSRDRKVAKSL
AVIVSIFGLCWAPYTLLMIIRAACHGHCVPDYWYETSFWLLWANSAVNPVLYPLCHHSFR
RAFTKLLCPQKLKIQPHSSLEHCWK

Sequence of entity 5 (S), FASTA

>9JEQ_5 ScFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Ligands and cofactors

ID	Name	Formula	Copies
HSM	Histamine	C5 H9 N3	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 P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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