8IHK: HCA3-Gi complex with acifran

Cryo-EM structure of HCA3-Gi complex with acifran (local). Determined by electron microscopy at 3.21 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 1
Atoms: 2,253
Mol. weight: 60.97 kDa
Ligands: P9X
Released: 30 Aug 2023

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

Secondary structure: helices and β-sheets

8IHK contains 14 α-helices and 4 β-strands across 1 chain. 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 R: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	1
α-helix	26-28	3
α-helix	30-54	25
α-helix	61-77	17
α-helix	80-88	9
α-helix	99-127	29
α-helix	135-138	4
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	268-279	12
α-helix	280-282	3
α-helix	283-290	8
α-helix	291-296	6

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)

Sequence of entity 1 (R), FASTA

>8IHK_1 Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3 (chains R)
MKTIIALSYIFCLVFADYKDDDDKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLNRHHLQDHFLEIDKKNCCVFRDDFIAKVLPPVLGLEFIFGLLGNGLALWI
FCFHLKSWKSSRIFLFNLAVADFLLIICLPFVMDYYVRRSDWKFGDIPCRLVLFMFAMNR
QGSIIFLTVVAVDRYFRVVHPHHALNKISNWTAAIISCLLWGITVGLTVHLLKKKLLIQN
GTANVCISFSICHTFRWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAIT
FIMVVAIVFVICFLPSVVVRIHIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDP
VVYYFSSPSFPNFFSTLINRCLQRKITGEPDNNRSTSVELTGDPNKTRGAPEALIANSGE
PWSPSYLGPTSNNHSKKGHCHQEPASLEKQLGCCIEENLYFQGSHHHHHH

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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