9IXX | pdb_00009ixx

Structural basis of the cysteinyl leukotriene receptor type 2 activation by LTD4

• PDB DOI: https://doi.org/10.2210/pdb9IXX/pdb
• EM Map EMD-60980: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Trichoplusia ni
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-07-29 Released: 2025-04-02 
• Deposition Author(s): Jiang, M., Xu, Y., Yin, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of the cysteinyl leukotriene receptor type 2 activation by LTD4.

Jiang, M., Xu, Y., Luan, X., Wu, K., Li, Z., Xu, H.E., Zhang, S., Jiang, Y., Yin, W.

(2025) Proc Natl Acad Sci U S A 122: e2417148122-e2417148122

• PubMed: 40193607 
• DOI: https://doi.org/10.1073/pnas.2417148122
• Primary Citation Related Structures: 
  9IXX


• PubMed Abstract: 
  

  The G protein-coupled cysteinyl leukotriene receptor CysLT2R plays intricate roles in the physiology and pathogenesis of inflammation-related processes. It has garnered increasing attention as a potential therapeutic target for atopic asthma, brain injury, central nervous system disorders, and various types of cancer. In this study, we present the cryo-electron microscopy structure of the cysteinyl leukotriene D4 (LTD4)-bound human CysLT2R in complex with a Gα _q protein, adopting an active conformation at a resolution of 3.15 Å. The structure elucidates a spacious polar pocket designed to accommodate the two branched negative ends of LTD4 and reveals a lateral ligand access route into the orthosteric pocket located on transmembrane domain helix (TM) 4 and 5. Furthermore, our findings highlight the crucial role of transmembrane domain helix 3 in sensing agonist moieties, representing the pivotal mechanism of receptor activation for both CysLT1R and CysLT2R. Collectively, the insights derived from our structural investigation establish a foundation for comprehending CysLT2R activation by its endogenous ligand LTD4, offering a rational basis for the design of drugs targeting CysLT2R.

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Organizational Affiliation: 
• Lingang Laboratory, Shanghai 200031, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
Department of Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China.
Center for Drug Research and Evaluation, National Infrastructures for Translational Medicine, Institute of Clinical Medicine, Peking Union Medical College Hospital, Beijing 100730, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong 528400, China.

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: 153.74 kDa 
• Atom Count: 9,036 
• Modeled Residue Count: 1,141 
• Deposited Residue Count: 1,368 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G-alpha q	A	361	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	351	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
scFv16	C [auth E]	248	Rattus norvegicus	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	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteinyl leukotriene receptor 2	E [auth R]	337	Homo sapiens	Mutation(s): 0  Gene Names: CYSLTR2, CYSLT2, CYSLT2R, PSEC0146 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NS75 (Homo sapiens) Explore Q9NS75  Go to UniProtKB:  Q9NS75
PHAROS:  Q9NS75 GTEx:  ENSG00000152207

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LTD (Subject of Investigation/LOI)	F [auth R]	(5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-azanyl-3-(2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid C25 H40 N2 O6 S YEESKJGWJFYOOK-IJHYULJSSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Jiang, M., Xu, Y., Yin, W.

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

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-04-30
  Changes: Data collection, Database references