7LJD

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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-021-00482-0
Primary Citation of Related Structures:
7LJC, 7LJD

Organizational Affiliation

The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21728
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered Gs protein alpha subunit	B [auth A]	246	Homo sapiens	Mutation(s): 0 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63092
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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 [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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54311
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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 [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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 35	E [auth N]	135	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G4C (Subject of Investigation/LOI) Query on G4C Download Ideal Coordinates CCD File SDF format, chain G [auth R] MOL2 format, chain G [auth R]	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		Interactions Focus chain G [auth R] Interactions & Density Focus chain G [auth R]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain H [auth R] SDF format, chain I [auth R] SDF format, chain J [auth R] SDF format, chain K [auth R] SDF format, chain L [auth R] MOL2 format, chain H [auth R] MOL2 format, chain I [auth R] MOL2 format, chain J [auth R] MOL2 format, chain K [auth R] MOL2 format, chain L [auth R]	H [auth R], I [auth R], J [auth R], K [auth R], L [auth R]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Focus chain K [auth R] Focus chain L [auth R] Interactions & Density Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Focus chain K [auth R] Focus chain L [auth R]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain M [auth R] SDF format, chain N [auth R] SDF format, chain O [auth R] SDF format, chain P [auth R] MOL2 format, chain M [auth R] MOL2 format, chain N [auth R] MOL2 format, chain O [auth R] MOL2 format, chain P [auth R]	M [auth R], N [auth R], O [auth R], P [auth R]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain M [auth R] Focus chain N [auth R] Focus chain O [auth R] Focus chain P [auth R] Interactions & Density Focus chain M [auth R] Focus chain N [auth R] Focus chain O [auth R] Focus chain P [auth R]
LDP Query on LDP Download Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R]	F [auth R]	L-DOPAMINE C₈ H₁₁ N O₂ VYFYYTLLBUKUHU-UHFFFAOYSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

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