7VUG | pdb_00007vug

Cryo-EM structure of a class A orphan GPCR in complex with Gi

• PDB DOI: https://doi.org/10.2210/pdb7VUG/pdb
• EM Map EMD-32127: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Niallia circulans
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-11-02 Released: 2021-12-29 
• Deposition Author(s): Liu, Z.J., Hua, T., Zhou, Y.L., Wu, L.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Literature

Molecular insights into ligand recognition and G protein coupling of the neuromodulatory orphan receptor GPR139.

Zhou, Y., Daver, H., Trapkov, B., Wu, L., Wu, M., Harpsoe, K., Gentry, P.R., Liu, K., Larionova, M., Liu, J., Chen, N., Brauner-Osborne, H., Gloriam, D.E., Hua, T., Liu, Z.J.

(2022) Cell Res 32: 210-213

• PubMed: 34916631 
• DOI: https://doi.org/10.1038/s41422-021-00591-w
• Primary Citation Related Structures: 
  7VUG, 7VUH, 7VUI, 7VUJ

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark.
Photobiology laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk, Russia.
Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark. [e-mail].
Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, 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: 175.18 kDa 
• Atom Count: 8,924 
• Modeled Residue Count: 1,127 
• Deposited Residue Count: 1,562 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	353	Homo sapiens	Mutation(s): 0  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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	346	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139	D [auth R]	533	Niallia circulans, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: xlnA, GPR139, GPRG1, PGR3 EC: 3.2.1.8 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P09850 (Niallia circulans) Explore P09850  Go to UniProtKB:  P09850
Find proteins for Q6DWJ6 (Homo sapiens) Explore Q6DWJ6  Go to UniProtKB:  Q6DWJ6
PHAROS:  Q6DWJ6 GTEx:  ENSG00000180269
UniProt Groups	P09850Q6DWJ6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E [auth S]	259	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7ZQ (Subject of Investigation/LOI)	F [auth R]	3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide C17 H17 Cl N2 O2 MWDVCHRYCKXEBY-LBPRGKRZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7ZQ	BindingDB:  7VUG	EC50: 16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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: 2021-12-29 
Deposition Author(s): Liu, Z.J., Hua, T., Zhou, Y.L., Wu, L.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2021-12-29
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.3: 2025-06-18
  Changes: Data collection