8IHJ: HCA3-Gi complex with acifran

Cryo-EM structure of HCA3-Gi complex with acifran. Determined by electron microscopy at 3.07 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 3.07 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,509
Mol. weight: 177.41 kDa
Ligands: P9X
Released: 30 Aug 2023

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

Secondary structure: helices and β-sheets

8IHJ contains 36 α-helices and 68 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-39	7	3
α-helix	46-53	8
β-strand	185-190	6	3
β-strand	195-200	6	3
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	3
α-helix	227-229	3
β-strand	233	1	4
β-strand	241	1	4
α-helix	242-254	13
β-strand	263-269	7	3
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-309	14
β-strand	319	1	3
β-strand	322-323	2	3
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	12
β-strand	58-63	6	13
β-strand	69-74	6	13
β-strand	78-83	6	13
β-strand	88-94	7	13
α-helix	95	1
β-strand	100-105	6	14
β-strand	111-116	6	14
β-strand	120-125	6	14
β-strand	134-140	7	14
β-strand	146-151	6	15
β-strand	157-161	5	15
β-strand	166-169	4	15
β-strand	176-180	5	15
β-strand	187-192	6	16
β-strand	198-203	6	16
β-strand	207-212	6	16
β-strand	218-223	6	16
β-strand	229-234	6	17
β-strand	240-245	6	17
β-strand	250-254	5	17
β-strand	259-264	6	17
β-strand	273-278	6	18
β-strand	284-289	6	18
β-strand	294-298	5	18
β-strand	303-308	6	18
β-strand	315-320	6	12
β-strand	327-331	5	12
β-strand	336-339	4	12

Chain C: 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 R: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	1
α-helix	24-27	4
α-helix	30-54	25
α-helix	61-77	17
α-helix	80-88	9
α-helix	99-126	28
α-helix	135-137	3
α-helix	141-157	17
α-helix	161-164	4
β-strand	169-171	3	2
β-strand	174-176	3	2
β-strand	182	1	1
α-helix	188-217	30
α-helix	226-259	34
α-helix	269-279	11
α-helix	281-290	10
α-helix	291-295	5

Chain S: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	5
β-strand	18-24	7	5
α-helix	29-31	3
β-strand	33-35	3	6
β-strand	38-39	2	7
β-strand	45-46	2	7
β-strand	49-51	3	6
β-strand	58-60	3	6
β-strand	68-73	6	5
α-helix	75-77	3
β-strand	78-83	6	5
β-strand	92-94	3	7
β-strand	97-99	3	6
β-strand	111	1	6
β-strand	115-117	3	7
β-strand	140	1	8
β-strand	146	1	9
β-strand	155-160	6	10
β-strand	161	1	8
β-strand	166	1	11
β-strand	172	1	11
β-strand	174-179	6	9
β-strand	186-190	5	9
β-strand	194-195	2	9
α-helix	196	1
β-strand	203-207	5	10
β-strand	211-216	6	10
α-helix	221-223	3
β-strand	226-231	6	9
β-strand	239	1	9
β-strand	244	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3	R	protein	530	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P49019 (AlphaFold model)
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

Sequence of entity 1 (R), FASTA

>8IHJ_1 Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3 (chains R)
MKTIIALSYIFCLVFADYKDDDDKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLNRHHLQDHFLEIDKKNCCVFRDDFIAKVLPPVLGLEFIFGLLGNGLALWI
FCFHLKSWKSSRIFLFNLAVADFLLIICLPFVMDYYVRRSDWKFGDIPCRLVLFMFAMNR
QGSIIFLTVVAVDRYFRVVHPHHALNKISNWTAAIISCLLWGITVGLTVHLLKKKLLIQN
GTANVCISFSICHTFRWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAIT
FIMVVAIVFVICFLPSVVVRIHIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDP
VVYYFSSPSFPNFFSTLINRCLQRKITGEPDNNRSTSVELTGDPNKTRGAPEALIANSGE
PWSPSYLGPTSNNHSKKGHCHQEPASLEKQLGCCIEENLYFQGSHHHHHH

Sequence of entity 2 (A), FASTA

>8IHJ_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVAAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYQEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (S), FASTA

>8IHJ_3 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 4 (B), FASTA

>8IHJ_4 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 5 (C), FASTA

>8IHJ_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Ligands and cofactors

ID	Name	Formula	Copies
P9X	(5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid	C12 H10 O4	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 P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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