7LJD | pdb_00007ljd

Allosteric modulator LY3154207 binding to dopamine-bound dopamine receptor 1 in complex with miniGs protein

• PDB DOI: https://doi.org/10.2210/pdb7LJD/pdb
• EM Map EMD-23391: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-01-28 Released: 2021-03-03 
• Deposition Author(s): Zhuang, Y., Krumm, B., Zhang, H., Zhou, X.E., Wang, Y., Guo, J., Huang, X.-P., Liu, Y., Wang, L., Cheng, X., Jiang, Y., Jiang, H., Melcher, K., Zhang, C., Yi, W., Roth, B.L., Zhang, Y., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor.

Zhuang, Y., Krumm, B., Zhang, H., Zhou, X.E., Wang, Y., Huang, X.P., Liu, Y., Cheng, X., Jiang, Y., Jiang, H., Zhang, C., Yi, W., Roth, B.L., Zhang, Y., Xu, H.E.

(2021) Cell Res 31: 593-596

• PubMed: 33750903 
• DOI: https://doi.org/10.1038/s41422-021-00482-0
• Primary Citation Related Structures: 
  7LJC, 7LJD

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Organizational Affiliation: 
• The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7365, USA.
Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.
MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.
Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand, Rapids, MI, USA.
State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
Key Laboratory of Molecular Target & Clinical Pharmacology, and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China.
Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7365, USA. [e-mail].
Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. [e-mail].
MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. [e-mail].
Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, 311121, China. [e-mail].
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 149.55 kDa 
• Atom Count: 8,518 
• Modeled Residue Count: 1,046 
• Deposited Residue Count: 1,303 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D(1A) dopamine receptor	A [auth R]	502	Homo sapiens	Mutation(s): 0  Gene Names: DRD1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P21728 (Homo sapiens) Explore P21728  Go to UniProtKB:  P21728
PHAROS:  P21728 GTEx:  ENSG00000184845

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered Gs protein alpha subunit	B [auth A]	246	Homo sapiens	Mutation(s): 0  EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092  Go to UniProtKB:  P63092
PHAROS:  P63092 GTEx:  ENSG00000087460

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	353	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D [auth G]	67	Bos taurus	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212  Go to UniProtKB:  P63212

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 35	E [auth N]	135	Lama glama	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4C (Subject of Investigation/LOI)	G [auth R]	2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone C24 H29 Cl2 N O3 XHCSBQBBGNQINS-DOTOQJQBSA-N
CLR	H [auth R], I [auth R], J [auth R], K [auth R], L [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM	M [auth R], N [auth R], O [auth R], P [auth R]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
LDP	F [auth R]	L-DOPAMINE C8 H11 N O2 VYFYYTLLBUKUHU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LDP	BindingDB:  7LJD	Ki: min: 7, max: 1.82e+4 (nM) from 29 assay(s)
		Kd: 2500 (nM) from 1 assay(s)
		IC50: min: 2, max: 1.00e+4 (nM) from 14 assay(s)
		EC50: min: 2.6, max: 5000 (nM) from 11 assay(s)
G4C	BindingDB:  7LJD	EC50: min: 1.1, max: 62 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Zhuang, Y., Krumm, B., Zhang, H., Zhou, X.E., Wang, Y., Guo, J., Huang, X.-P., Liu, Y., Wang, L., Cheng, X., Jiang, Y., Jiang, H., Melcher, K., Zhang, C., Yi, W., Roth, B.L., Zhang, Y., Xu, H.E.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81922071
National Natural Science Foundation of China (NSFC)	China	31770796
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	RO1MH112205
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM128641

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references
• Version 1.2: 2021-05-12
  Changes: Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary