9E51 | pdb_00009e51

Cryo-EM structure of human LPHN2 (ADGRL2)/G13 complex in lipid nanodiscs

• PDB DOI: https://doi.org/10.2210/pdb9E51/pdb
• EM Map EMD-47522: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-10-26 Released: 2025-11-12 
• Deposition Author(s): He, F., Skiniotis, G.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of G13-bound human LPHN2 (ADGRL2) in lipid nanodiscs

He, F., Skiniotis, G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 109.52 kDa 
• Atom Count: 6,978 
• Modeled Residue Count: 882 
• Deposited Residue Count: 966 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Guanine nucleotide-binding protein subunit alpha-13	A [auth B]	230	Homo sapiens	Mutation(s): 0  Gene Names: GNA13
UniProt & NIH Common Fund Data Resources
Find proteins for Q14344 (Homo sapiens) Explore Q14344  Go to UniProtKB:  Q14344
PHAROS:  Q14344 GTEx:  ENSG00000120063

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B [auth C]	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 [auth D]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
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
Adhesion G protein-coupled receptor L2	D [auth A]	325	Homo sapiens	Mutation(s): 0  Gene Names: ADGRL2, KIAA0786, LEC1, LPHH1, LPHN2
UniProt & NIH Common Fund Data Resources
Find proteins for O95490 (Homo sapiens) Explore O95490  Go to UniProtKB:  O95490
PHAROS:  O95490 GTEx:  ENSG00000117114

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR (Subject of Investigation/LOI)	E [auth A], F [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

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	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): He, F., Skiniotis, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	5R01DK132902-02

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release