7YFD: Engineered G-alpha-q

Cryo-EM structure of the imetit-bound histamine H4 receptor and Gq complex. Determined by electron microscopy at 3.1 Å resolution. Released 25 Oct 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Mus musculus, Lama glama
Chains: 6
Atoms: 9,934
Mol. weight: 196.75 kDa
Ligands: ITF, CLR
Released: 25 Oct 2023

Explore 7YFD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YFD contains 34 α-helices and 71 β-strands across 6 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-39	6	1
α-helix	46-56	11
β-strand	184-191	8	1
β-strand	194-201	8	1
β-strand	220-226	7	1
α-helix	233-245	13
β-strand	253-259	7	1
α-helix	261-269	9
α-helix	275-277	3
α-helix	280-282	3
α-helix	293-294	2
α-helix	299-318	20
β-strand	326-330	5	1
α-helix	339-357	19

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	45-51	7	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-307	4	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-341	6	2

Chain C: 1 helix, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	17-25	9	9
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	9
β-strand	78-84	7	9
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-117	3	11
β-strand	118-119	2	10
β-strand	141	1	12
β-strand	146-148	3	13
β-strand	155-160	6	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
β-strand	203-208	6	12
β-strand	211-216	6	12
β-strand	225-231	7	13
β-strand	238-239	2	13
β-strand	243-246	4	13

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-22	15
α-helix	30-41	12
α-helix	45-47	3
α-helix	56-58	3

Chain N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	17-25	9	15
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	68-73	6	15
β-strand	78-84	7	15
α-helix	88-90	3
β-strand	92-98	7	17
β-strand	118	1	17
β-strand	122-124	3	17
β-strand	125-126	2	16

Chain R: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	13-43	31
α-helix	49-63	15
α-helix	64-68	5
α-helix	69-76	8
α-helix	85-117	33
α-helix	120	1
α-helix	121-125	5
α-helix	130-157	28
α-helix	168-170	3
α-helix	172-179	8
α-helix	180-184	5
α-helix	185-203	19
α-helix	299-328	30
α-helix	339-357	19
α-helix	363-372	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Engineered G-alpha-q	A	protein	361	Homo sapiens	P63092 (AlphaFold model), P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	388	Homo sapiens	P62873 (AlphaFold model)
scFv16	C	protein	259	Mus musculus
Histamine H4 receptor	R	protein	548	Homo sapiens	Q9H3N8 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768
Nb35	N	protein	129	Lama glama

Sequence of entity 1 (A), FASTA

>7YFD_1 Engineered G-alpha-q (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNL
V

Sequence of entity 2 (B), FASTA

>7YFD_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNID
PVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSS
WVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIV
TSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMC
RQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSF
SKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKI
WNGSSGGGGSGGGGSSGVSGWRLFKKIS

Sequence of entity 3 (C), FASTA

>7YFD_3 scFv16 (chains C)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 4 (R), FASTA

>7YFD_4 Histamine H4 receptor (chains R)
MPDTNSTINLSLSTRVTLAFFMSLVAFAIMLGNALVILAFVVDKNLRHRSSYFFLNLAIS
DFFVGVISIPLYIPHTLFEWDFGKEICVFWLTTDYLLCTASVYNIVLISYDRYLSVSNAV
SYRTQHTGVLKIVTLMVAVWVLAFLVNGPMILVSESWKDEGSECEPGFFSEWYILAITSF
LEFVIPVILVAYFNMNIYWSLWKRDHLSRCQSHPGLTAVSSNICGHSFRGRLSSRRSLSA
STEVPASFHSERQRRKSSLMFSSRTKMNSNTIASKMGSFSQSDSVALHQREHVELLRARR
LAKSLAILLGVFAVCWAPYSLFTIVLSFYSSATGPKSVWYRIAFWLQWFNSFVNPLLYPL
CHKRFQKAFLKIFCIKKQPLPSQHSRSVSSVFTLEDFVGDWEQTAAYNLDQVLEQGGVSS
LLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFK
VILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSM
LFRVTINS

Sequence of entity 5 (G), FASTA

>7YFD_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (N), FASTA

>7YFD_6 Nb35 (chains N)
MQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASIS
YTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRG
QGTQVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
ITF	2-(1~{H}-imidazol-5-yl)ethyl carbamimidothioate	C6 H10 N4 S	1
CLR	Cholesterol	C27 H46 O	2

Primary citation

Structural insights into the agonists binding and receptor selectivity of human histamine H 4 receptor. Im, D., Kishikawa, J.I., Shiimura, Y. et al. Nat Commun (2023) 14:6538-6538. DOI 10.1038/s41467-023-42260-z · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
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
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

Browse structure collections

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