Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 86.22 kDa 
• Atom Count: 5870 
• Modelled Residue Count: 729 
• Deposited Residue Count: 752 
• Unique protein chains: 1

6A94

Crystal structure of 5-HT2AR in complex with zotepine

• PDB DOI: 10.2210/pdb6A94/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-07-11 Released: 2019-02-13 
• Deposition Author(s): Kimura, T.K., Asada, H., Inoue, A., Kadji, F.M.N., Im, D., Mori, C., Arakawa, T., Hirata, K., Nomura, Y., Nomura, N., Aoki, J., Iwata, S., Shimamura, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.269 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 

Literature

Structures of the 5-HT2Areceptor in complex with the antipsychotics risperidone and zotepine.

Kimura, K.T., Asada, H., Inoue, A., Kadji, F.M.N., Im, D., Mori, C., Arakawa, T., Hirata, K., Nomura, Y., Nomura, N., Aoki, J., Iwata, S., Shimamura, T.

(2019) Nat Struct Mol Biol 26: 121-128

• PubMed: 30723326 
• DOI: 10.1038/s41594-018-0180-z
• Primary Citation of Related Structures:  
  6A93, 6A94


• PubMed Abstract: 
  

Many drugs target the serotonin 2A receptor (5-HT _2A R), including second-generation antipsychotics that also target the dopamine D ₂ receptor (D ₂ R). These drugs often produce severe side effects due to non-selective binding to other aminergic receptors. Here, we report the structures of human 5-HT _2A R in complex with the second-generation antipsychotics risperidone and zotepine. These antipsychotics effectively stabilize the inactive conformation by forming direct contacts with the residues at the bottom of the ligand-binding pocket, the movements of which are important for receptor activation. 5-HT _2A R is structurally similar to 5-HT _2C R but possesses a unique side-extended cavity near the orthosteric binding site. A docking study and mutagenic studies suggest that a highly 5-HT _2A R-selective antagonist binds the side-extended cavity. The conformation of the ligand-binding pocket in 5-HT _2A R significantly differs around extracellular loops 1 and 2 from that in D ₂ R. These findings are beneficial for the rational design of safer antipsychotics and 5-HT _2A R-selective drugs.

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Organizational Affiliation: 

Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2A,Soluble cytochrome b562	A, B	376	Homo sapiens, Escherichia coli	Mutation(s): 6  Gene Names: HTR2A, HTR2, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28223 (Homo sapiens) Explore P28223  Go to UniProtKB:  P28223
PHAROS:  P28223 GTEx:  ENSG00000102468
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
UniProt Groups	P0ABE7P28223

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	D [auth A], I [auth B]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
A6L	J [auth B]	2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-KTKRTIGZSA-N
ZOT	C [auth A], G [auth B]	2-(3-chloranylbenzo[b][1]benzothiepin-5-yl)oxy-N,N-dimethyl-ethanamine C18 H18 Cl N O S HDOZVRUNCMBHFH-UHFFFAOYSA-N
PLM	H [auth B]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
1PE	E [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.269 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 279.18	α = 90
b = 42.22	β = 92.16
c = 91.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-07-11 
• Released Date: 2019-02-13 
Deposition Author(s): Kimura, T.K., Asada, H., Inoue, A., Kadji, F.M.N., Im, D., Mori, C., Arakawa, T., Hirata, K., Nomura, Y., Nomura, N., Aoki, J., Iwata, S., Shimamura, T.

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references