8JPN | pdb_00008jpn

Cryo-EM structure of succinate receptor bound to cis-epoxysuccinic acid coupling to Gi

• PDB DOI: https://doi.org/10.2210/pdb8JPN/pdb
• EM Map EMD-36484: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli, Oplophorus gracilirostris
• Expression System: 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: 2.90 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 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 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 195.26 kDa 
• Atom Count: 8,557 
• Modeled Residue Count: 1,157 
• Deposited Residue Count: 1,746 
• 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	354	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	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	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 EC: 1.13.12.13 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
Find proteins for Q9GV45 (Oplophorus gracilirostris) Explore Q9GV45  Go to UniProtKB:  Q9GV45
UniProt Groups	P0ABE7Q9BXA5Q9GV45

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E [auth S]	286	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U9S (Subject of Investigation/LOI)	F [auth R]	(2R,3S)-oxirane-2,3-dicarboxylic acid C4 H4 O5 DCEMCPAKSGRHCN-XIXRPRMCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 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: 2024-10-30
  Changes: Data collection, Structure summary