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- EMDB-45616: CryoEM Structure of HCA2 DREADD Gi1 in complex with FCH-2296413 (... -

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Basic information

Entry
Database: EMDB / ID: EMD-45616
TitleCryoEM Structure of HCA2 DREADD Gi1 in complex with FCH-2296413 (Local Refinement)
Map data
Sample
  • Complex: Mouse HCAD-Gai1 in complex with FCH-2296413
    • Protein or peptide: Hydroxycarboxylic acid receptor 2
  • Ligand: (3M,4aR,5aR)-3-(1H-tetrazol-5-yl)-4,4a,5,5a-tetrahydro-1H-cyclopropa[4,5]cyclopenta[1,2-c]pyrazole
KeywordsGPCR / HCA2 / MEMBRANE PROTEIN / DREADD
Function / homology
Function and homology information


Hydroxycarboxylic acid-binding receptors / Class A/1 (Rhodopsin-like receptors) / nicotinic acid receptor activity / positive regulation of neutrophil apoptotic process / purinergic nucleotide receptor activity / G alpha (i) signalling events / positive regulation of adiponectin secretion / negative regulation of lipid catabolic process / G protein-coupled receptor activity / G protein-coupled receptor signaling pathway ...Hydroxycarboxylic acid-binding receptors / Class A/1 (Rhodopsin-like receptors) / nicotinic acid receptor activity / positive regulation of neutrophil apoptotic process / purinergic nucleotide receptor activity / G alpha (i) signalling events / positive regulation of adiponectin secretion / negative regulation of lipid catabolic process / G protein-coupled receptor activity / G protein-coupled receptor signaling pathway / apoptotic process / GTP binding / membrane / 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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsKrumm BE / Kang HJ / Diberto JF / Kapolka NJ / Gumpper RH / Olsen RHJ / Huang XP / Zhang S / Fay JF / Roth BL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)5R01MH112205 United States
CitationJournal: Cell / Year: 2024
Title: Structure-guided design of a peripherally restricted chemogenetic system.
Authors: Hye Jin Kang / Brian E Krumm / Adrien Tassou / Matan Geron / Jeffrey F DiBerto / Nicholas J Kapolka / Ryan H Gumpper / Kensuke Sakamoto / D Dewran Kocak / Reid H J Olsen / Xi-Ping Huang / ...Authors: Hye Jin Kang / Brian E Krumm / Adrien Tassou / Matan Geron / Jeffrey F DiBerto / Nicholas J Kapolka / Ryan H Gumpper / Kensuke Sakamoto / D Dewran Kocak / Reid H J Olsen / Xi-Ping Huang / Shicheng Zhang / Karen L Huang / Saheem A Zaidi / MyV T Nguyen / Min Jeong Jo / Vsevolod Katritch / Jonathan F Fay / Grégory Scherrer / Bryan L Roth /
Abstract: Designer receptors exclusively activated by designer drugs (DREADDs) are chemogenetic tools for remotely controlling cellular signaling, neural activity, behavior, and physiology. Using a structure- ...Designer receptors exclusively activated by designer drugs (DREADDs) are chemogenetic tools for remotely controlling cellular signaling, neural activity, behavior, and physiology. Using a structure-guided approach, we provide a peripherally restricted Gi-DREADD, hydroxycarboxylic acid receptor DREADD (HCAD), whose native receptor is minimally expressed in the brain, and a chemical actuator that does not cross the blood-brain barrier (BBB). This was accomplished by combined mutagenesis, analoging via an ultra-large make-on-demand library, structural determination of the designed DREADD receptor via cryoelectron microscopy (cryo-EM), and validation of HCAD function. Expression and activation of HCAD in dorsal root ganglion (DRG) neurons inhibit action potential (AP) firing and reduce both acute and tissue-injury-induced inflammatory pain. The HCAD chemogenetic system expands the possibilities for studying numerous peripheral systems with little adverse effects on the central nervous system (CNS). The structure-guided approach used to generate HCAD also has the potential to accelerate the development of emerging chemogenetic tools for basic and translational sciences.
History
DepositionJul 3, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45616.png

Downloads & links

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Map

FileDownload / File: emd_45616.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-7.5176644 - 11.041248
Average (Standard dev.)-0.0058212564 (±0.11635534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 225.27998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite Map

Fileemd_45616_additional_1.map
AnnotationComposite Map
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Half map: #2

Fileemd_45616_half_map_1.map
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Half map: #1

Fileemd_45616_half_map_2.map
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Sample components

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Entire : Mouse HCAD-Gai1 in complex with FCH-2296413

EntireName: Mouse HCAD-Gai1 in complex with FCH-2296413
Components
  • Complex: Mouse HCAD-Gai1 in complex with FCH-2296413
    • Protein or peptide: Hydroxycarboxylic acid receptor 2
  • Ligand: (3M,4aR,5aR)-3-(1H-tetrazol-5-yl)-4,4a,5,5a-tetrahydro-1H-cyclopropa[4,5]cyclopenta[1,2-c]pyrazole

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Supramolecule #1: Mouse HCAD-Gai1 in complex with FCH-2296413

SupramoleculeName: Mouse HCAD-Gai1 in complex with FCH-2296413 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Hydroxycarboxylic acid receptor 2

MacromoleculeName: Hydroxycarboxylic acid receptor 2 / type: protein_or_peptide / ID: 1
Details: Protein starts at M1, GTT sequence from protease cleavage site, Mutation D120A, Mutation R108K to convert WT to DREADD.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 34.247727 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDHFLVINGK NCCVFRDENI AKVLPPVLGL EFVFGLLGNG LALWIFCFHL KSWKSSRIFL FNLAVADFLL IICLPFLTDN YVHNWDWRF GGIPCRVMLF MLAMNKQGSI IFLTVVAVAR YFRVVHPHHF LNKISNRTAA IISCFLWGLT IGLTVHLLYT N MMTKNGEA ...String:
SDHFLVINGK NCCVFRDENI AKVLPPVLGL EFVFGLLGNG LALWIFCFHL KSWKSSRIFL FNLAVADFLL IICLPFLTDN YVHNWDWRF GGIPCRVMLF MLAMNKQGSI IFLTVVAVAR YFRVVHPHHF LNKISNRTAA IISCFLWGLT IGLTVHLLYT N MMTKNGEA YLCSSFSICY NFRWHDAMFL LEFFLPLAII LFCSGRIIWS LRQRQMDRHA KIKRAINFIM VVAIVFIICF LP SVAVRIR IFWLLYKYNV RNCDIYSSVD LAFFTTLSFT YMNSMLDPVV YYFSSPS

UniProtKB: Hydroxycarboxylic acid receptor 2

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Macromolecule #2: (3M,4aR,5aR)-3-(1H-tetrazol-5-yl)-4,4a,5,5a-tetrahydro-1H-cyclopr...

MacromoleculeName: (3M,4aR,5aR)-3-(1H-tetrazol-5-yl)-4,4a,5,5a-tetrahydro-1H-cyclopropa[4,5]cyclopenta[1,2-c]pyrazole
type: ligand / ID: 2 / Number of copies: 1 / Formula: XI9
Molecular weightTheoretical: 188.189 Da

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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

Concentration3.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xk2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 250000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9cib:
CryoEM Structure of HCA2 DREADD Gi1 in complex with FCH-2296413 (Local Refinement)

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