8PKM | pdb_00008pkm

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  PDBTMMemProtMD


• 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 5-HT_1A receptor agonist for the treatment of pain

Ullrich, A., Schneider, J., Braz, J.M., Neu, E., Staffen, N., Stanek, M., Blahova, J., Hove, T., Albert, T., Allikalt, A., Lober, S., Bhardwaj, K., Rodriguez-Rosado, S., Fink, E., Rasmussen, T., Hubner, H., Inoue, A., Shoichet, B.K., Basbaum, A.J., Bottcher, B., Weikert, D., Gmeiner, P.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.09.11.557127

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 
• Modeled 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 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	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

Binding Affinity Annotations
ID	Source	Binding Affinity
ZKV	BindingDB:  8PKM	Ki: min: 0.4, max: 1 (nM) from 3 assay(s)
		EC50: min: 23, max: 26 (nM) from 2 assay(s)

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
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.2: 2024-12-18
  Changes: Data collection, Database references