8JPP | pdb_00008jpp

Cryo-EM structure of succinate receptor bound to succinate acid coupling MiniGsq

• PDB DOI: https://doi.org/10.2210/pdb8JPP/pdb
• EM Map EMD-36486: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli, Oplophorus gracilirostris
• Expression System: Trichoplusia ni, Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-06-12 Released: 2024-05-22 
• Deposition Author(s): Wang, T.X., Tang, W.Q., Li, F.H., Wang, J.Y.
• 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 activation and G protein coupling selectivity of human succinate receptor SUCR1.

Wang, T., Tang, W., Zhu, X., Lv, Z., Chen, J., Li, Y., Sun, X., Lv, H., Gu, Q., Li, F., Wang, J.

(2024) Cell Res 34: 590-593

• PubMed: 38744983 
• DOI: https://doi.org/10.1038/s41422-024-00968-7
• Primary Citation of Related Structures:  
  8JPN, 8JPP

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China.
Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 153.27 kDa 
• Atom Count: 7,137 
• Modeled Residue Count: 922 
• Deposited Residue Count: 1,359 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	253	Homo sapiens	Mutation(s): 0  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	377	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
Soluble cytochrome b562,Succinate receptor 1,Oplophorus-luciferin 2-monooxygenase catalytic subunit	D [auth R]	658	Escherichia coli, Homo sapiens, Oplophorus gracilirostris This entity is chimeric	Mutation(s): 0  Gene Names: cybC, SUCNR1, GPR91 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q9BXA5 (Homo sapiens) Explore Q9BXA5  Go to UniProtKB:  Q9BXA5
PHAROS:  Q9BXA5 GTEx:  ENSG00000198829
UniProt Groups	P0ABE7Q9BXA5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	E [auth R]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N

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: 2024-05-22 
Deposition Author(s): Wang, T.X., Tang, W.Q., Li, F.H., Wang, J.Y.

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

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release
  
• Version 1.1: 2024-08-14
  Changes: Data collection, Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary