8ZQE | pdb_00008zqe

Cryo-EM structure of the GPR15L(C11)-bound GPR15 complex

• PDB DOI: https://doi.org/10.2210/pdb8ZQE/pdb
• EM Map EMD-60384: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-06-02 Released: 2024-07-10 
• Deposition Author(s): Zhang, Z.Y., Zheng, Y., Xu, F.
• 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 recognition of the atypical chemokine-like peptide GPR15L by its cognate receptor GPR15.

Zhang, Z., Zheng, Y., Xu, L., Yue, Y., Xu, K., Li, F., Xu, F.

(2024) Cell Discov 10: 69-69

• PubMed: 38918398 
• DOI: https://doi.org/10.1038/s41421-024-00698-5
• Primary Citation of Related Structures:  
  8ZQE

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Shanghai Clinical Research and Trial Center, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 217.87 kDa 
• Atom Count: 8,767 
• Modeled Residue Count: 1,131 
• Deposited Residue Count: 1,961 
• Unique protein chains: 6

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	340	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	97	Homo sapiens	Mutation(s): 0  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
scFv16	D [auth S]	279	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
GPR15	E [auth R]	881	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P49685 (Homo sapiens) Explore P49685  Go to UniProtKB:  P49685
PHAROS:  P49685 GTEx:  ENSG00000154165
UniProt Groups	P0ABE7P49685P0AEX9

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein GPR15LG	F [auth L]	10	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UWK7 (Homo sapiens) Explore Q6UWK7  Go to UniProtKB:  Q6UWK7
PHAROS:  Q6UWK7 GTEx:  ENSG00000188373

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 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: 2024-07-10 
Deposition Author(s): Zhang, Z.Y., Zheng, Y., Xu, F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071194

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.2: 2024-11-27
  Changes: Data collection
• Version 1.3: 2025-06-18
  Changes: Data collection