8IHI: HCA2-Gi complex with acifran

Cryo-EM structure of HCA2-Gi complex with acifran. Determined by electron microscopy at 3.11 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 3.11 Å
Organisms: Homo sapiens, synthetic construct, Mus musculus
Chains: 5
Atoms: 8,665
Mol. weight: 191.73 kDa
Ligands: P9X, NAG
Released: 30 Aug 2023

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

Secondary structure: helices and β-sheets

8IHI contains 33 α-helices and 67 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-39	6	1
α-helix	46-53	8
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	331-351	21

Chain B: 4 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	47-51	5	10
β-strand	58-63	6	11
β-strand	69-74	6	11
β-strand	78-83	6	11
β-strand	88-94	7	11
β-strand	100-105	6	12
β-strand	111-116	6	12
β-strand	120-125	6	12
β-strand	134-140	7	12
β-strand	146-151	6	13
β-strand	156-161	6	13
β-strand	166-170	5	13
β-strand	175-180	6	13
β-strand	187-192	6	14
β-strand	198-203	6	14
β-strand	207-212	6	14
β-strand	220-223	4	14
β-strand	229-234	6	15
β-strand	240-245	6	15
β-strand	250-254	5	15
β-strand	259-264	6	15
α-helix	272	1
β-strand	273-278	6	16
β-strand	284-289	6	16
β-strand	294-298	5	16
β-strand	303-308	6	16
β-strand	315-320	6	10
β-strand	327-331	5	10
β-strand	336-339	4	10

Chain C: 4 helices, 0 β-strands

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

Chain R: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	17
β-strand	17-19	3	17
α-helix	25-54	30
α-helix	61-77	17
α-helix	80-88	9
α-helix	98-127	30
α-helix	135-138	4
α-helix	141-157	17
α-helix	160-162	3
β-strand	169-171	3	18
β-strand	174-176	3	18
β-strand	182-183	2	17
α-helix	188-217	30
α-helix	224-260	37
α-helix	270-280	11
α-helix	281-283	3
α-helix	285-290	6
α-helix	291-295	5

Chain S: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	3
β-strand	18-24	7	3
α-helix	29-31	3
β-strand	33-35	3	4
β-strand	38-39	2	5
β-strand	45-46	2	5
β-strand	49-51	3	4
β-strand	58-60	3	4
α-helix	62-64	3
β-strand	68-73	6	3
β-strand	78-83	6	3
β-strand	92-94	3	5
β-strand	97-99	3	4
β-strand	111	1	4
β-strand	115-117	3	5
β-strand	140	1	6
β-strand	146	1	7
β-strand	155-160	6	8
β-strand	161	1	6
β-strand	166	1	9
β-strand	172	1	9
β-strand	174-179	6	7
β-strand	185-190	6	7
β-strand	194-195	2	7
α-helix	196	1
β-strand	203-207	5	8
β-strand	211-216	6	8
β-strand	226-231	6	7
β-strand	243-244	2	7

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)
scFv16	S	protein	248	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	382	Mus musculus	P62874 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	70	Mus musculus	P63213 (AlphaFold model)
Soluble cytochrome b562,Hydroxycarboxylic acid receptor 2	R	protein	658	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), Q8TDS4

Sequence of entity 1 (A), FASTA

>8IHI_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVAAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYQEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (S), FASTA

>8IHI_2 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 3 (B), FASTA

>8IHI_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHENLYFQGSSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQ
MRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCA
YAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDT
TCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTG
HESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRL
LLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGGSG
GGGSGGSSSGGVSGWRLFKKIS

Sequence of entity 4 (C), FASTA

>8IHI_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 5 (R), FASTA

>8IHI_5 Soluble cytochrome b562,Hydroxycarboxylic acid receptor 2 (chains R)
MKTIIALSYIFCLVFADYKDDDDKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLNRHHLQDHFLEIDKKNCCVFRDDFIVKVLPPVLGLEFIFGLLGNGLALWI
FCFHLKSWKSSRIFLFNLAVADFLLIICLPFLMDNYVRRWDWKFGDIPCRLMLFMLAMNR
QGSIIFLTVVAVDRYFRVVHPHHALNKISNRTAAIISCLLWGITIGLTVHLLKKKMPIQN
GGANLCSSFSICHTFQWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAIT
FIMVVAIVFVICFLPSVVVRIRIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDP
VVYYFSSPSFPNFFSTLINRCLQRKMTGEPDNNRSTSVELTGDPNKTRGAPEALMANSGE
PWSPSYLGPTSPENLYFQGSVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVT
PIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVI
DGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Ligands and cofactors

ID	Name	Formula	Copies
P9X	(5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid	C12 H10 O4	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding. Suzuki, S., Tanaka, K., Nishikawa, K. et al. Nat Commun (2023) 14:5899-5899. DOI 10.1038/s41467-023-41650-7 · PubMed

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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