7VUI | pdb_00007vui

Cryo-EM structure of a class A orphan GPCR

• PDB DOI: https://doi.org/10.2210/pdb7VUI/pdb
• EM Map EMD-32129: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Niallia circulans
• Expression System: Escherichia coli, 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 Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 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 of 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: 155.14 kDa 
• Atom Count: 8,287 
• Modeled Residue Count: 1,034 
• Deposited Residue Count: 1,368 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	261	Homo sapiens	Mutation(s): 4  Gene Names: GNAS, GNAS1, GSP 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: 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 [auth G]	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
Nanobody 35	D [auth N]	157	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139	E [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	Q6DWJ6P09850

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	F [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
7ZQ (Subject of Investigation/LOI)	H [auth R]	3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide C17 H17 Cl N2 O2 MWDVCHRYCKXEBY-LBPRGKRZSA-N
MG	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 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 Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2021-12-29
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection