8JXX: Clobenpropit-bound H4R/Gi complex

Clobenpropit-bound H4R/Gi complex. Determined by electron microscopy at 3.06 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 3.06 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,493
Mol. weight: 157.35 kDa
Ligands: VCL
Released: 20 Mar 2024

Explore 8JXX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JXX contains 37 α-helices and 61 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 B: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-39	6	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
α-helix	257-259	3
β-strand	264-269	6	1
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-320	2	1
β-strand	323	1	1
α-helix	330-350	21

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
α-helix	30-32	3
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-153	8	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	176-181	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
α-helix	272-273	2
β-strand	276-278	3	9
β-strand	284-287	4	9
β-strand	294-298	5	9
β-strand	306-308	3	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain E: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-12	3	11
β-strand	15-24	10	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-86	9	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-119	5	11
β-strand	141-143	3	12
β-strand	147-148	2	13
β-strand	155-162	8	12
β-strand	167	1	14
β-strand	173	1	14
β-strand	175-180	6	13
β-strand	187-191	5	13
β-strand	195-196	2	13
β-strand	204-209	6	12
β-strand	212-218	7	12
β-strand	226-232	7	13
α-helix	238	1
β-strand	240	1	13
β-strand	244-246	3	13

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	15-42	28
α-helix	49-62	14
α-helix	63-65	3
α-helix	68-77	10
α-helix	84-117	34
α-helix	119-123	5
α-helix	130-145	16
α-helix	148-152	5
α-helix	167-170	4
α-helix	172-179	8
α-helix	180-184	5
α-helix	185-202	18
α-helix	294-329	36
α-helix	338-348	11
α-helix	350-361	12
α-helix	364-370	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histamine H4 receptor	R	protein	390	Homo sapiens	Q9H3N8 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	247	Homo sapiens

Sequence of entity 1 (R), FASTA

>8JXX_1 Histamine H4 receptor (chains R)
MPDTNSTINLSLSTRVTLAFFMSLVAFAIMLGNALVILAFVVDKNLRHRSSYFFLNLAIS
DFFVGVISIPLYIPHTLFEWDFGKEICVFWLTTDYLLCTASVYNIVLISYDRYLSVSNAV
SYRTQHTGVLKIVTLMVAVWVLAFLVNGPMILVSESWKDEGSECEPGFFSEWYILAITSF
LEFVIPVILVAYFNMNIYWSLWKRDHLSRCQSHPGLTAVSSNICGHSFRGRLSSRRSLSA
STEVPASFHSERQRRKSSLMFSSRTKMNSNTIASKMGSFSQSDSVALHQREHVELLRARR
LAKSLAILLGVFAVCWAPYSLFTIVLSFYSSATGPKSVWYRIAFWLQWFNSFVNPLLYPL
CHKRFQKAFLKIFCIKKQPLPSQHSRSVSS

Sequence of entity 2 (B), FASTA

>8JXX_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>8JXX_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>8JXX_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>8JXX_5 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
VCL	3-(1~{H}-imidazol-4-yl)propyl ~{N}'-[(4-chlorophenyl)methyl]carbamimidothioate	C14 H17 Cl N4 S	1

Primary citation

Structural basis of ligand recognition and design of antihistamines targeting histamine H 4 receptor. Xia, R., Shi, S., Xu, Z. et al. Nat Commun (2024) 15:2493-2493. DOI 10.1038/s41467-024-46840-5 · PubMed

Other PDB entries of the same protein (UniProt Q9H3N8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9JED 2.58 Å, Cryo-EM structure of Histamine-bound Histamine receptor 4 H4R G protein complex
8YNA 2.63 Å, Cryo-EM structure of histamine H4 receptor in complex with immepip and Gi
9LRC 2.84 Å, Cryo-EM structure of the histamine H4 receptor-Gi protein complex (Receptor focused)
9LRE 2.84 Å, Cryo-EM structure of the histamine H4 receptor-Gi protein complex (Overall)
9L42 2.9 Å, Cryo-EM structure of human histamine receptor H4R in complex with agonist histamine and…
7YFC 3.0 Å, Cryo-EM structure of the histamine-bound histamine H4 receptor and Gq complex
8HN8 3.0 Å, Cryo-EM structure of ligand histamine-bound Histamine H4 receptor Gi complex
8HOC 3.0 Å, Cryo-EM structure of ligand histamine-bound Histamine H4 receptor Gi complex
8JXW 3.01 Å, VUF6884-bound H4R/Gi complex
8JXT 3.07 Å, Histamine-bound H4R/Gi complex
7YFD 3.1 Å, Cryo-EM structure of the imetit-bound histamine H4 receptor and Gq complex

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