8UTD | pdb_00008utd

CryoEM Structure of HCA2-Gi1 in complex with MK-1903

• PDB DOI: https://doi.org/10.2210/pdb8UTD/pdb
• EM Map EMD-42538: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Lama glama
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2023-10-30 Released: 2025-02-26 
• Deposition Author(s): Krumm, B.E., Kang, H.J., Diberto, J.F., Kapolka, N.J., Gumpper, R.H., Olsen, R.H.J., Huang, X.P., Zhang, S., Fay, J.F., Roth, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-guided design of a peripherally restricted chemogenetic system.

Kang, H.J., Krumm, B.E., Tassou, A., Geron, M., DiBerto, J.F., Kapolka, N.J., Gumpper, R.H., Sakamoto, K., Dewran Kocak, D., Olsen, R.H.J., Huang, X.P., Zhang, S., Huang, K.L., Zaidi, S.A., Nguyen, M.T., Jo, M.J., Katritch, V., Fay, J.F., Scherrer, G., Roth, B.L.

(2024) Cell 187: 7433-7449.e20

• PubMed: 39631393 
• DOI: https://doi.org/10.1016/j.cell.2024.11.001
• Primary Citation Related Structures: 
  8UTD, 8UUJ, 9CIB


• PubMed 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-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.

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Organizational Affiliation: 
• Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Cell Biology and Physiology, UNC Neuroscience Center, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; National Institute of Mental Health Psychoactive Drug Screening Program (NIMH-PDSP), School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Quantitative and Computational Biology, Department of Chemistry, Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA.
Department of Cell Biology and Physiology, UNC Neuroscience Center, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: [e-mail].
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 158.86 kDa 
• Atom Count: 8,872 
• Modeled Residue Count: 1,138 
• Deposited Residue Count: 1,418 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxycarboxylic acid receptor 2	A [auth R]	368	Homo sapiens	Mutation(s): 1  Gene Names: HCAR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDS4 (Homo sapiens) Explore Q8TDS4  Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4 GTEx:  ENSG00000182782

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	B [auth D]	267	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	C [auth A]	354	Homo sapiens	Mutation(s): 2  Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	358	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth C]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XOT (Subject of Investigation/LOI)	F [auth R]	(4aR,5aR)-4,4a,5,5a-tetrahydro-1H-cyclopropa[4,5]cyclopenta[1,2-c]pyrazole-3-carboxylic acid C8 H8 N2 O2 CUTZNERBKDMLAP-QWWZWVQMSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Krumm, B.E., Kang, H.J., Diberto, J.F., Kapolka, N.J., Gumpper, R.H., Olsen, R.H.J., Huang, X.P., Zhang, S., Fay, J.F., Roth, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	5R01MH112205

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release
  
• Version 1.1: 2025-05-14
  Changes: Data collection