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- EMDB-36901: Cryo-EM structure of Acipimox bound human hydroxy-carboxylic acid... -

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Basic information

Entry
Database: EMDB / ID: EMD-36901
TitleCryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 (Local refinement)
Map datasharpening map
Sample
  • Complex: Acipimox bound human hydroxy-carboxylic acid receptor 2
    • Protein or peptide: Human hydroxycarboxylic acid receptor 2
  • Ligand: 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid
KeywordsGPCR / G-Protein / MEMBRANE PROTEIN / acipimox / signaling
Function / homology
Function and homology information


nicotinic acid receptor activity / neutrophil apoptotic process / Hydroxycarboxylic acid-binding receptors / positive regulation of neutrophil apoptotic process / Class A/1 (Rhodopsin-like receptors) / positive regulation of adiponectin secretion / negative regulation of lipid catabolic process / cell junction / G alpha (i) signalling events / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
: / 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
Hydroxycarboxylic acid receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsPark JH / Ishimoto N / Park SY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2.
Authors: Jae-Hyun Park / Kouki Kawakami / Naito Ishimoto / Tatsuya Ikuta / Mio Ohki / Toru Ekimoto / Mitsunori Ikeguchi / Dong-Sun Lee / Young-Ho Lee / Jeremy R H Tame / Asuka Inoue / Sam-Yong Park /
Abstract: Hydroxycarboxylic acid receptors (HCAR1, HCAR2, and HCAR3) transduce G signaling upon biding to molecules such as lactic acid, butyric acid and 3-hydroxyoctanoic acid, which are associated with ...Hydroxycarboxylic acid receptors (HCAR1, HCAR2, and HCAR3) transduce G signaling upon biding to molecules such as lactic acid, butyric acid and 3-hydroxyoctanoic acid, which are associated with lipolytic and atherogenic activity, and neuroinflammation. Although many reports have elucidated the function of HCAR2 and its potential as a therapeutic target for treating not only dyslipidemia but also neuroimmune disorders such as multiple sclerosis and Parkinson's disease, the structural basis of ligand recognition and ligand-induced G-coupling remains unclear. Here we report three cryo-EM structures of the human HCAR2-G signaling complex, each bound with different ligands: niacin, acipimox or GSK256073. All three agonists are held in a deep pocket lined by residues that are not conserved in HCAR1 and HCAR3. A distinct hairpin loop at the HCAR2 N-terminus and extra-cellular loop 2 (ECL2) completely enclose the ligand. These structures also reveal the agonist-induced conformational changes propagated to the G-protein-coupling interface during activation. Collectively, the structures presented here are expected to help in the design of ligands specific for HCAR2, leading to new drugs for the treatment of various diseases such as dyslipidemia and inflammation.
History
DepositionJul 21, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36901.png

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Map

FileDownload / File: emd_36901.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpening map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 200 pix.
= 249. Å		1.25 Å/pix.
x 200 pix.
= 249. Å		1.25 Å/pix.
x 200 pix.
= 249. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
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Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.7389991 - 2.7505782
Average (Standard dev.)-0.0015437141 (±0.040952552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36901_msk_1.map
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Additional map: map

Fileemd_36901_additional_1.map
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Half map: half map 2

Fileemd_36901_half_map_1.map
Annotationhalf map 2
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Half map: half map 1

Fileemd_36901_half_map_2.map
Annotationhalf map 1
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Sample components

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Entire : Acipimox bound human hydroxy-carboxylic acid receptor 2

EntireName: Acipimox bound human hydroxy-carboxylic acid receptor 2
Components
  • Complex: Acipimox bound human hydroxy-carboxylic acid receptor 2
    • Protein or peptide: Human hydroxycarboxylic acid receptor 2
  • Ligand: 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid

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Supramolecule #1: Acipimox bound human hydroxy-carboxylic acid receptor 2

SupramoleculeName: Acipimox bound human hydroxy-carboxylic acid receptor 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Human hydroxycarboxylic acid receptor 2

MacromoleculeName: Human hydroxycarboxylic acid receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.320297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGAPADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKV KEAQAAAEQL KTTRNAYIQK YLEFMNRHHL QDHFLEIDKK NCCVFRDDFI VKVLPPVLGL EFIFGLLGNG L ALWIFCFH ...String:
GPGAPADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKV KEAQAAAEQL KTTRNAYIQK YLEFMNRHHL QDHFLEIDKK NCCVFRDDFI VKVLPPVLGL EFIFGLLGNG L ALWIFCFH LKSWKSSRIF LFNLAVADFL LIICLPFLMD NYVRRWDWKF GDIPCRLMLF MLAMNRQGSI IFLTVVAVDR YF RVVHPHH ALNKISNRTA AIISCLLWGI TIGLTVHLLK KKMPIQNGGA NLCSSFSICH TFQWHEAMFL LEFFLPLGII LFC SARIIW SLRQRQMDRH AKIKRAITFI MVVAIVFVIC FLPSVVVRIR IFWLLHTSGT QNCEVYRSVD LAFFITLSFT YMNS MLDPV VYYFSSPSFP NFFSTLINRC LQRKMTGEPD NNRSTSVELT GDPNKTRGAP EALMANSGEP WSPSYLGPTS P

UniProtKB: Hydroxycarboxylic acid receptor 2

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Macromolecule #2: 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid

MacromoleculeName: 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: OJX
Molecular weightTheoretical: 155.131 Da
Chemical component information

ChemComp-OJX:
5-methyl-4-oxidanyl-pyrazin-4-ium-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

BufferpH: 7.5
Details: 20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 228127
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8k5c:
Cryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 (Local refinement)

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