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- EMDB-35447: Cryo-EM structure of HCA3-Gi complex with acifran (local) -

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Basic information

Entry
Database: EMDB / ID: EMD-35447
TitleCryo-EM structure of HCA3-Gi complex with acifran (local)
Map datamap
Sample
  • Complex: Multiprotein complex
    • Protein or peptide: Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3
  • Ligand: (5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid
KeywordsGPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


nicotinic acid receptor activity / Hydroxycarboxylic acid-binding receptors / electron transport chain / G protein-coupled receptor activity / cell junction / G alpha (i) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding ...nicotinic acid receptor activity / Hydroxycarboxylic acid-binding receptors / electron transport chain / G protein-coupled receptor activity / cell junction / G alpha (i) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / plasma membrane
Similarity search - Function
: / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Soluble cytochrome b562 / Hydroxycarboxylic acid receptor 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsSuzuki S / Nishikawa K / Suzuki H / Fujiyoshi Y
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00451 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding.
Authors: Shota Suzuki / Kotaro Tanaka / Kouki Nishikawa / Hiroshi Suzuki / Atsunori Oshima / Yoshinori Fujiyoshi /
Abstract: Hydroxycarboxylic acid receptors (HCA) are expressed in various tissues and immune cells. HCA2 and its agonist are thus important targets for treating inflammatory and metabolic disorders. Only ...Hydroxycarboxylic acid receptors (HCA) are expressed in various tissues and immune cells. HCA2 and its agonist are thus important targets for treating inflammatory and metabolic disorders. Only limited information is available, however, on the active-state binding of HCAs with agonists. Here, we present cryo-EM structures of human HCA2-Gi and HCA3-Gi signaling complexes binding with multiple compounds bound. Agonists were revealed to form a salt bridge with arginine, which is conserved in the HCA family, to activate these receptors. Extracellular regions of the receptors form a lid-like structure that covers the ligand-binding pocket. Although transmembrane (TM) 6 in HCAs undergoes dynamic conformational changes, ligands do not directly interact with amino acids in TM6, suggesting that indirect signaling induces a slight shift in TM6 to activate Gi proteins. Structural analyses of agonist-bound HCA2 and HCA3 together with mutagenesis and molecular dynamics simulation provide molecular insights into HCA ligand recognition and activation mechanisms.
History
DepositionFeb 22, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35447.png

Downloads & links

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Map

FileDownload / File: emd_35447.map.gz / Format: CCP4 / Size: 37.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 214 pix.
= 166.92 Å		0.78 Å/pix.
x 214 pix.
= 166.92 Å		0.78 Å/pix.
x 214 pix.
= 166.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.78 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.2181531 - 1.8434094
Average (Standard dev.)0.0015022873 (±0.034390897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions214214214
Spacing214214214
CellA=B=C: 166.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35447_msk_1.map
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Half map: half map A

Fileemd_35447_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_35447_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : Multiprotein complex

EntireName: Multiprotein complex
Components
  • Complex: Multiprotein complex
    • Protein or peptide: Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3
  • Ligand: (5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid

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Supramolecule #1: Multiprotein complex

SupramoleculeName: Multiprotein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3

MacromoleculeName: Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.749406 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LNRHHLQDHF LEIDKKNCCV FRDDFIAKVL P PVLGLEFI ...String:
MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LNRHHLQDHF LEIDKKNCCV FRDDFIAKVL P PVLGLEFI FGLLGNGLAL WIFCFHLKSW KSSRIFLFNL AVADFLLIIC LPFVMDYYVR RSDWKFGDIP CRLVLFMFAM NR QGSIIFL TVVAVDRYFR VVHPHHALNK ISNWTAAIIS CLLWGITVGL TVHLLKKKLL IQNGTANVCI SFSICHTFRW HEA MFLLEF FLPLGIILFC SARIIWSLRQ RQMDRHAKIK RAITFIMVVA IVFVICFLPS VVVRIHIFWL LHTSGTQNCE VYRS VDLAF FITLSFTYMN SMLDPVVYYF SSPSFPNFFS TLINRCLQRK ITGEPDNNRS TSVELTGDPN KTRGAPEALI ANSGE PWSP SYLGPTSNNH SKKGHCHQEP ASLEKQLGCC IEENLYFQGS HHHHHH

UniProtKB: Soluble cytochrome b562, Hydroxycarboxylic acid receptor 3

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Macromolecule #2: (5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid

MacromoleculeName: (5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: P9X
Molecular weightTheoretical: 218.205 Da
Chemical component information

ChemComp-P9X:
(5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration15 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95567
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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