7EXD

Lasmiditan-bound serotonin 1F (5-HT1F) receptor-Gi protein complex

• PDB DOI: https://doi.org/10.2210/pdb7EXD/pdb
• EM Map EMD-31371: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus, Escherichia coli
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-05-27 Released: 2021-08-04 
• Deposition Author(s): Huang, S., Xu, P., Jiang, Y., Xu, H.E.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for recognition of anti-migraine drug lasmiditan by the serotonin receptor 5-HT 1F -G protein complex.

Huang, S., Xu, P., Tan, Y., You, C., Zhang, Y., Jiang, Y., Xu, H.E.

(2021) Cell Res 31: 1036-1038

• PubMed: 34239069 
• DOI: https://doi.org/10.1038/s41422-021-00527-4
• Primary Citation of Related Structures:  
  7EXD

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Organizational Affiliation: 

The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 170.65 kDa 
• Atom Count: 8,749 
• Modelled Residue Count: 1,118 
• Deposited Residue Count: 1,524 
• 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	345	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 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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth E]	248	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,5-hydroxytryptamine receptor 1F	E [auth R]	506	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: cybC, HTR1F, HTR1EL Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P30939 (Homo sapiens) Explore P30939  Go to UniProtKB:  P30939
PHAROS:  P30939 GTEx:  ENSG00000179097
UniProt Groups	P0ABE7P30939

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
05X (Subject of Investigation/LOI)	F [auth R]	2,4,6-tris(fluoranyl)-N-[6-(1-methylpiperidin-4-yl)carbonylpyridin-2-yl]benzamide C19 H18 F3 N3 O2 XEDHVZKDSYZQBF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
05X	BindingDB:  7EXD	Ki: 2.2 (nM) from 1 assay(s)
		IC50: 88 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Huang, S., Xu, P., Jiang, Y., Xu, H.E.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFA0507002

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary