8YKV | pdb_00008ykv

Cryo-EM structure of succinate receptor SUCR1 bound to compound 31

• PDB DOI: https://doi.org/10.2210/pdb8YKV/pdb
• EM Map EMD-39373: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Rattus norvegicus, synthetic construct, Bos taurus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-03-05 Released: 2024-05-29 
• Deposition Author(s): Li, C., Liu, H., Li, J., Zhu, H., Fu, W., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis of ligand recognition and activation of the human succinate receptor SUCR1.

Li, C., Liu, H., Li, J., He, X., Zhu, H., Fu, W., Xu, H.E.

(2024) Cell Res 34: 594-596

• PubMed: 38834763 
• DOI: https://doi.org/10.1038/s41422-024-00984-7
• Primary Citation of Related Structures:  
  8YKV, 8YKW, 8YKX

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Organizational Affiliation: 
• The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Lingang Laboratory, Shanghai, China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
University of Chinese Academy of Sciences, Beijing, China.
School of Pharmacy, Fudan University, Shanghai, China.
School of Pharmacy, Fudan University, Shanghai, China. [e-mail].
The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Lingang Laboratory, Shanghai, China. [e-mail].
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China. [e-mail].
University of 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: 151.13 kDa 
• Atom Count: 8,665 
• Modeled Residue Count: 1,110 
• Deposited Residue Count: 1,346 
• 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): 4  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	340	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment ScFv16	C [auth E]	247	synthetic construct	Mutation(s): 0

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]	71	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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate receptor 1	E [auth R]	334	Homo sapiens	Mutation(s): 0  Gene Names: SUCNR1, GPR91 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXA5 (Homo sapiens) Explore Q9BXA5  Go to UniProtKB:  Q9BXA5
PHAROS:  Q9BXA5 GTEx:  ENSG00000198829

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LYV	F [auth R]	(2~{S})-2-[[6-[4-(trifluoromethyloxy)phenyl]pyridin-2-yl]carbonylamino]butanedioic acid C17 H13 F3 N2 O6 TUTOXIPIHTUWDS-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Li, C., Liu, H., Li, J., Zhu, H., Fu, W., Xu, H.E.

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

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Data collection, Database references
• Version 1.2: 2024-08-14
  Changes: Data collection, Database references