8HOC: PDB entry 8HOC

Cryo-EM structure of ligand histamine-bound Histamine H4 receptor Gi complex. Determined by electron microscopy at 3.0 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,918
Mol. weight: 180.49 kDa
Ligands: ITF
Released: 20 Dec 2023

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

Secondary structure: helices and β-sheets

8HOC contains 37 α-helices and 60 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
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
α-helix	228-230	3
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
α-helix	262	1
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	300-309	10
β-strand	319-324	6	1
α-helix	331-350	20

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
α-helix	38-39	2
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	89-94	6	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
α-helix	145	1
β-strand	146-151	6	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	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	260-264	5	8
β-strand	273-278	6	9
α-helix	280-282	3
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-41	12
α-helix	53-55	3

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	14-42	29
α-helix	51-63	13
α-helix	64-68	5
α-helix	69-76	8
α-helix	84-117	34
α-helix	119-123	5
α-helix	129-154	26
α-helix	172-179	8
α-helix	180-184	5
α-helix	185-204	20
α-helix	293-327	35
α-helix	334-336	3
α-helix	338-357	20
α-helix	365-373	9

Chain S: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	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	69-73	5	10
β-strand	78-84	7	10
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-119	5	11
β-strand	129	1	12
β-strand	134	1	13
β-strand	143-147	5	14
β-strand	148	1	12
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	13
β-strand	174-178	5	13
β-strand	182-183	2	13
α-helix	184	1
β-strand	191-196	6	14
β-strand	199-204	6	14
α-helix	209-211	3
β-strand	214-219	6	13
α-helix	226-228	3
β-strand	231-232	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Soluble cytochrome b562, Histamine H4 receptor fusion	R	protein	549	Homo sapiens	P0ABE7 (AlphaFold model), Q9H3N8
Single-chain variable fragment scFv16	S	protein	297	Homo sapiens

Sequence of entity 1 (A), FASTA

>8HOC_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8HOC_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>8HOC_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8HOC_4 Soluble cytochrome b562, Histamine H4 receptor fusion (chains R)
MKTIIALSYIFCLVFAHHHHHHHHHHDYKDDDDKENLYFQSGAPADLEDNWETLNDNLKV
IEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDAL
KLANEGKVKEAQAAAEQLKTTRNAYIQKYLEFLEVLFQGPSATNSTINLSLSTRITLAFL
MSLLAFAIMLGNAVVILAFVVDKNLRHRSNYFFLNLAISDFFVGVISIPLYIPHTLFEWD
FGKEICVFWLTTDYLLCTASVYNIVLISYDRYQSVSNAVSYRTQHTGILKIVTLMVAVWV
LAFLVNGPMILVSESWKDEGSECEPGFFSEWYILAITSFLEFLVPVILVAYFNMYIYWSL
WKRGNLSRCQSHPGLTSVSSSICGHSFRGRLFSRTSLPASKEVAASFHSERQRRKSSLLF
SLRTQMNSNIIASKMGSLSQSDSLALHQREHLELLRARKLAKSLAILLGVFAVCWAPYSL
FTIVLSFYPSATRPKSVWYRIAFWLQWFNSFVNPFLYPLCHKRFQKAFLKIFCIKKQPIP
SQHNRSVSS

Sequence of entity 5 (S), FASTA

>8HOC_5 Single-chain variable fragment scFv16 (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKLSC
SASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQ
MTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ITF	2-(1~{H}-imidazol-5-yl)ethyl carbamimidothioate	C6 H10 N4 S	1

Primary citation

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.

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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