8E9W | pdb_00008e9w

CryoEM structure of miniGq-coupled hM3Dq in complex with DCZ

PDB DOI: https://doi.org/10.2210/pdb8E9W/pdb
EM Map EMD-27966: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2022-08-27 Released: 2022-11-30
Deposition Author(s): Zhang, S., Fay, J.F., Roth, B.L.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Molecular basis for selective activation of DREADD-based chemogenetics.

Zhang, S., Gumpper, R.H., Huang, X.P., Liu, Y., Krumm, B.E., Cao, C., Fay, J.F., Roth, B.L.

(2022) Nature 612: 354-362

PubMed: 36450989 Search on PubMed
DOI: https://doi.org/10.1038/s41586-022-05489-0
Primary Citation Related Structures:
8E9W, 8E9X, 8E9Y, 8E9Z, 8EA0

PubMed Abstract:
Designer receptors exclusively activated by designer drugs (DREADDs) represent a powerful chemogenetic technology for the remote control of neuronal activity and cellular signalling ^1-4. The muscarinic receptor-based DREADDs are the most widely used chemogenetic tools in neuroscience research. The G _q-coupled DREADD (hM3Dq) is used to enhance neuronal activity, whereas the G _i/o-coupled DREADD (hM4Di) is utilized to inhibit neuronal activity ⁵. Here we report four DREADD-related cryogenic electron microscopy high-resolution structures: a hM3Dq-miniG _q complex and a hM4Di-miniG _o complex bound to deschloroclozapine; a hM3Dq-miniG _q complex bound to clozapine-N-oxide; and a hM3R-miniG _q complex bound to iperoxo. Complemented with mutagenesis, functional and computational simulation data, our structures reveal key details of the recognition of DREADD chemogenetic actuators and the molecular basis for activation. These findings should accelerate the structure-guided discovery of next-generation chemogenetic tools.

Organizational Affiliation

Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Macromolecule Content

Total Structure Weight: 141.79 kDa
Atom Count: 8,529
Modeled Residue Count: 1,123
Deposited Residue Count: 1,272
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muscarinic acetylcholine receptor M3	A	365	Homo sapiens	Mutation(s): 2 Gene Names: CHRM3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P20309 (Homo sapiens) Explore P20309 Go to UniProtKB: P20309
PHAROS: P20309 GTEx: ENSG00000133019
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20309
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
miniGq	B	246	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	339	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E	251	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WEC (Subject of Investigation/LOI) Query on WEC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	11-(4-methylpiperazin-1-yl)-5H-dibenzo[b,e][1,4]diazepine C₁₈ H₂₀ N₄ VQHITFFJBFOMBG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
WEC	BindingDB: 8E9W	IC50: min: 31, max: 39 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-30

Deposition Author(s):

Zhang, S.

Fay, J.F.

Roth, B.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	U24DK1169195
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	Psychoactive Drug Screening (PDSP)