8PKM

Befiradol-bound serotonin 5-HT1A receptor - Gi Protein Complex

• PDB DOI: https://doi.org/10.2210/pdb8PKM/pdb
• EM Map EMD-17747: EMDB EMDataResource

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


• Deposited: 2023-06-27 Released: 2024-05-29 
• Deposition Author(s): Schneider, J., Gmeiner, P., Hove, T.T., Rasmussen, T., Boettcher, B.
• Funding Organization(s): iNEXT-Discovery, German Research Foundation (DFG)

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Experimental Data Snapshot

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

Literature

Discovery of a functionally selective serotonin 1A receptor agonist for the treatment of pain

Boettcher, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 140.25 kDa 
• Atom Count: 6,929 
• Modelled Residue Count: 874 
• Deposited Residue Count: 1,243 
• Unique protein chains: 4

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 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	352	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
5-hydroxytryptamine receptor 1A	D [auth R]	466	Homo sapiens	Mutation(s): 0  Gene Names: HTR1A, ADRB2RL1, ADRBRL1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08908 (Homo sapiens) Explore P08908  Go to UniProtKB:  P08908
PHAROS:  P08908 GTEx:  ENSG00000178394

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T7M	F [auth R]	(2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate C46 H82 O16 P2 WSLBJQQQZZTFBA-NPJVAJNNSA-N
ZKV (Subject of Investigation/LOI)	G [auth R]	(3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyridin-2-yl)methylamino]methyl]piperidin-1-yl]methanone C20 H22 Cl F2 N3 O PKZXLMVXBZICTF-UHFFFAOYSA-N
CLR	E [auth R]	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
RECONSTRUCTION	cryoSPARC	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Schneider, J., Gmeiner, P., Hove, T.T., Rasmussen, T., Boettcher, B.

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Funding Organization	Location	Grant Number
iNEXT-Discovery	European Union	24759
German Research Foundation (DFG)	Germany	INST 93/903-1
German Research Foundation (DFG)	Germany	INST 93/1042-1

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release