8IHB: HCA2-Gi complex with GSK256073

Cryo-EM structure of HCA2-Gi complex with GSK256073. Determined by electron microscopy at 2.85 Å resolution. Released 13 Sept 2023.

Method: Electron microscopy
Resolution: 2.85 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,708
Mol. weight: 191.7 kDa
Ligands: OKL, NAG
Released: 13 Sept 2023

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

Secondary structure: helices and β-sheets

8IHB contains 36 α-helices and 70 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	7-30	24
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	208-210	3
α-helix	212-215	4
β-strand	220-226	7	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	319-323	5	3
α-helix	331-351	21

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	14
β-strand	58-63	6	15
β-strand	69-74	6	15
β-strand	78-83	6	15
β-strand	89-94	6	15
β-strand	100-105	6	16
β-strand	111-116	6	16
β-strand	120-125	6	16
β-strand	134-140	7	16
β-strand	146-151	6	17
β-strand	156-161	6	17
β-strand	166-170	5	17
β-strand	175-180	6	17
β-strand	187	1	18
β-strand	191-192	2	19
β-strand	198-202	5	19
β-strand	203	1	18
β-strand	207-212	6	19
β-strand	218-223	6	19
β-strand	229-234	6	20
β-strand	240-245	6	20
β-strand	249-254	6	20
β-strand	259-265	7	20
α-helix	272	1
β-strand	273-278	6	21
β-strand	284-289	6	21
β-strand	294-298	5	21
β-strand	303-308	6	21
β-strand	317-320	4	14
β-strand	327-330	4	14
β-strand	336-339	4	14

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: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	16-19	4	1
α-helix	24-27	4
α-helix	30-54	25
α-helix	61-77	17
α-helix	80-87	8
α-helix	98-129	32
α-helix	135-138	4
α-helix	141-157	17
α-helix	161-164	4
β-strand	170-171	2	2
β-strand	174-175	2	2
β-strand	182-183	2	1
α-helix	188-195	8
α-helix	198-217	20
α-helix	224-260	37
α-helix	270-280	11
α-helix	285-290	6
α-helix	291-295	5

Chain S: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	5
β-strand	18-23	6	6
α-helix	29-31	3
β-strand	33-35	3	7
β-strand	38-39	2	8
β-strand	45-46	2	8
β-strand	49-51	3	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
β-strand	92-94	3	8
β-strand	97-99	3	7
β-strand	110-111	2	7
β-strand	115-117	3	8
β-strand	118	1	5
β-strand	140	1	9
β-strand	146	1	10
β-strand	156-160	5	11
β-strand	161	1	9
β-strand	166	1	12
β-strand	172	1	12
β-strand	174-179	6	13
β-strand	185-190	6	13
β-strand	194-195	2	13
α-helix	196	1
β-strand	203-207	5	11
β-strand	211-216	6	11
α-helix	221-223	3
β-strand	226-231	6	13
β-strand	244	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Hydroxycarboxylic acid receptor 2	R	protein	658	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), Q8TDS4 (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	69	Mus musculus	P63213

Sequence of entity 1 (R), FASTA

>8IHB_1 Soluble cytochrome b562,Hydroxycarboxylic acid receptor 2 (chains R)
MKTIIALSYIFCLVFADYKDDDDKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLNRHHLQDHFLEIDKKNCCVFRDDFIVKVLPPVLGLEFIFGLLGNGLALWI
FCFHLKSWKSSRIFLFNLAVADFLLIICLPFLMDNYVRRWDWKFGDIPCRLMLFMLAMNR
QGSIIFLTVVAVDRYFRVVHPHHALNKISNRTAAIISCLLWGITIGLTVHLLKKKMPIQN
GGANLCSSFSICHTFQWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAIT
FIMVVAIVFVICFLPSVVVRIRIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDP
VVYYFSSPSFPNFFSTLINRCLQRKMTGEPDNNRSTSVELTGDPNKTRGAPEALMANSGE
PWSPSYLGPTSPENLYFQGSVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVT
PIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVI
DGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 2 (A), FASTA

>8IHB_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVAAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYQEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (S), FASTA

>8IHB_3 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 4 (B), FASTA

>8IHB_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

>8IHB_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
SNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR
EKKFFCAIL

Ligands and cofactors

ID	Name	Formula	Copies
OKL	8-chloranyl-3-pentyl-7H-purine-2,6-dione	C10 H13 Cl N4 O2	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 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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