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9as9

Local refinement of 5-HT2AR bound to RS130-180 in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM)

Method: ELECTRON MICROSCOPY Dmax: 64.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

5-hydroxytryptamine receptor 2A

Homo sapiens

UniProt P28223

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–471 Not recorded A1AFX 2,5-dimethoxy-N,N-dimethyl-4-{2-[({2-[(prop-2-yn-1-yl)oxy]phenyl}methyl)amino]ethyl}aniline × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.47 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9AS9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6A93 Crystal structure of 5-HT2AR in complex with risperidone Deposited 2018-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–265（196 aa）
Chain A 313–403（91 aa）
Mutation：S162K, M164W, R120I, H124I, R128G, M29W Mutation：S162K, M164W, R120I, H124I, R128G, M29W 8NU 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one × 1 CLR CHOLESTEROL × 1 ZN ZINC ION × 1 1PE PENTAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO
Resolution 3.00 Å R-free 0.275
6A93 Crystal structure of 5-HT2AR in complex with risperidone Deposited 2018-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 70–265（196 aa）
Chain B 313–403（91 aa）
Mutation：S162K, M164W, R120I, H124I, R128G, M29W Mutation：S162K, M164W, R120I, H124I, R128G, M29W 8NU 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one × 1 CLR CHOLESTEROL × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO
Resolution 3.00 Å R-free 0.275
6A94 Crystal structure of 5-HT2AR in complex with zotepine Deposited 2018-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–265（196 aa）
Chain A 313–403（91 aa）
Mutation：S162K, M164W,R120I, H124I, R128G, M29W Mutation：S162K, M164W,R120I, H124I, R128G, M29W ZOT 2-(3-chloranylbenzo[b][1]benzothiepin-5-yl)oxy-N,N-dimethyl-ethanamine × 1 CLR CHOLESTEROL × 1 1PE PENTAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES, pH 6.0, or HEPES, pH 7.0, 30% (v/v) PEG400, 100 mM Li-chloride, Na-acetate, or 14 other various salts from StockOptions Salt (Hampton Research)
Resolution 2.90 Å R-free 0.269
6A94 Crystal structure of 5-HT2AR in complex with zotepine Deposited 2018-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 70–265（196 aa）
Chain B 313–403（91 aa）
Mutation：S162K, M164W,R120I, H124I, R128G, M29W Mutation：S162K, M164W,R120I, H124I, R128G, M29W ZOT 2-(3-chloranylbenzo[b][1]benzothiepin-5-yl)oxy-N,N-dimethyl-ethanamine × 1 CLR CHOLESTEROL × 1 PLM PALMITIC ACID × 1 A6L 2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES, pH 6.0, or HEPES, pH 7.0, 30% (v/v) PEG400, 100 mM Li-chloride, Na-acetate, or 14 other various salts from StockOptions Salt (Hampton Research)
Resolution 2.90 Å R-free 0.269
6WGT Crystal structure of HTR2A with hallucinogenic agonist Deposited 2020-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–265（200 aa）
Chain A 311–405（95 aa）
Not recorded 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 CLR CHOLESTEROL × 2 OLA OLEIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293.15 K；100 mM Tris (pH7.0) 370-410 mM KPO4-mono 90-120 mM GuHCl 28-34% PEG 400
Resolution 3.40 Å R-free 0.305
6WGT Crystal structure of HTR2A with hallucinogenic agonist Deposited 2020-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 66–265（200 aa）
Chain B 311–405（95 aa）
Not recorded 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 OLA OLEIC ACID × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293.15 K；100 mM Tris (pH7.0) 370-410 mM KPO4-mono 90-120 mM GuHCl 28-34% PEG 400
Resolution 3.40 Å R-free 0.305
6WGT Crystal structure of HTR2A with hallucinogenic agonist Deposited 2020-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 66–265（200 aa）
Chain C 311–405（95 aa）
Not recorded 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PO4 PHOSPHATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293.15 K；100 mM Tris (pH7.0) 370-410 mM KPO4-mono 90-120 mM GuHCl 28-34% PEG 400
Resolution 3.40 Å R-free 0.305
6WH4 Crystal structure of HTR2A with inverse agonist Deposited 2020-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–265（200 aa）
Chain A 311–405（95 aa）
Not recorded 89F 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine × 1 OLA OLEIC ACID × 2 CLR CHOLESTEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293.15 K；100 mM Tris (pH7.0) 380 mM potassium phosphate-monobasic 33% PEG 400 100 mM Guanidine HCL 300 mM NDSB-195
Resolution 3.40 Å R-free 0.304
6WH4 Crystal structure of HTR2A with inverse agonist Deposited 2020-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 66–265（200 aa）
Chain B 311–405（95 aa）
Not recorded 89F 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine × 1 OLA OLEIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293.15 K；100 mM Tris (pH7.0) 380 mM potassium phosphate-monobasic 33% PEG 400 100 mM Guanidine HCL 300 mM NDSB-195
Resolution 3.40 Å R-free 0.304
6WH4 Crystal structure of HTR2A with inverse agonist Deposited 2020-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 66–265（200 aa）
Chain C 311–405（95 aa）
Not recorded 89F 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine × 1 OLA OLEIC ACID × 1 CLR CHOLESTEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 NDS ETHYL DIMETHYL AMMONIO PROPANE SULFONATE × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293.15 K；100 mM Tris (pH7.0) 380 mM potassium phosphate-monobasic 33% PEG 400 100 mM Guanidine HCL 300 mM NDSB-195
Resolution 3.40 Å R-free 0.304
6WHA HTR2A bound to 25-CN-NBOH in complex with a mini-Galpha-q protein, beta/gamma subunits and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM) Deposited 2020-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 66–404（339 aa） Fragment：cybC (UNP residues 23-127) + linker + HTR2A (UNP residues 66-404)
Not recorded U0G 4-(2-{[(2-hydroxyphenyl)methyl]amino}ethyl)-2,5-dimethoxybenzonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
7RAN 5-HT2AR bound to a novel agonist in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM) Deposited 2021-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 66–404（339 aa） Fragment：UNP residues 66-404
Not recorded 3IQ (3R)-3-methyl-5-(1H-pyrrolo[2,3-b]pyridin-3-yl)-1,2,3,6-tetrahydropyridin-1-ium × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
7VOD Crystal structure of 5-HT2AR in complex with cariprazine Deposited 2021-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–265（196 aa）
Chain A 313–403（91 aa）
Mutation：S162K,N164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,N164W,M1007W,R1098I,H1102I,R1106G,S372N MG MAGNESIUM ION × 1 CLR CHOLESTEROL × 3 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 3 7RU 3-[4-[2-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Tris/HCl, 100 mM Potassium formate, 30% PEG
Resolution 3.30 Å R-free 0.239
7VOE Crystal structure of 5-HT2AR in complex with aripiprazole Deposited 2021-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–265（196 aa）
Chain A 313–403（91 aa）
Mutation：S162K,N164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,N164W,M1007W,R1098I,H1102I,R1106G,S372N CLR CHOLESTEROL × 3 1PE PENTAETHYLENE GLYCOL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 9SC 7-[4-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]butoxy]-3,4-dihydro-1H-quinolin-2-one × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Tris/HCl, 50 mM ammonium floride, 28%-30% PEG400, 300 mM NDSB-195 or 3% w/v trimethylamine N-oxide dihydrate
Resolution 2.90 Å R-free 0.244
7WC4 Crystal structure of serotonin 2A receptor in complex with serotonin Deposited 2021-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 67–265（199 aa）
Chain A 313–403（91 aa）
Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N CLR CHOLESTEROL × 3 1PE PENTAETHYLENE GLYCOL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 3 MG MAGNESIUM ION × 1 SRO SEROTONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Tris-HCl , 100 mM sodium acetate trihydrate, 30% (v/v) polyethylene glycol 400 (PEG400), 4% (v/v) Polypropylene glycol P 400
Resolution 3.20 Å R-free 0.261
7WC5 Crystal structure of serotonin 2A receptor in complex with psilocin Deposited 2021-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 67–265（199 aa）
Chain A 313–403（91 aa）
Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N MG MAGNESIUM ION × 1 CLR CHOLESTEROL × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 3 91Q 3-[2-(dimethylamino)ethyl]-1~{H}-indol-4-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Tris-HCl, 175 mM sodium acetate trihydrate, 30% (v/v) PEG400, 4% (v/v) Polypropylene glycol P 400
Resolution 3.20 Å R-free 0.257
7WC6 Crystal structure of serotonin 2A receptor in complex with LSD Deposited 2021-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 67–265（199 aa）
Chain A 313–403（91 aa）
Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N MG MAGNESIUM ION × 1 CLR CHOLESTEROL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 1PE PENTAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Tris-HCl, 40 mM Potassium formate, 30% (v/v) PEG400, 2% (v/v) Polypropylene glycol P 400
Resolution 2.60 Å R-free 0.263
7WC7 Crystal structure of serotonin 2A receptor in complex with lisuride Deposited 2021-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 67–265（199 aa）
Chain A 313–403（91 aa）
Not recorded MG MAGNESIUM ION × 1 CLR CHOLESTEROL × 1 1PE PENTAETHYLENE GLYCOL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 5 PEG DI(HYDROXYETHYL)ETHER × 3 H8G N,N-diethyl-N'-[(8alpha)-6-methyl-9,10-didehydroergolin-8-yl]urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293.15 K；100 mM Tris-HCl, 75 mM sodium acetate trihydrate, 30% (v/v) PEG400, 4% (v/v) Polypropylene glycol P 400
Resolution 2.60 Å R-free 0.256
7WC8 Crystal structure of serotonin 2A receptor in complex with lumateperone Deposited 2021-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 67–265（199 aa）
Chain A 313–403（91 aa）
Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N MG MAGNESIUM ION × 1 CLR CHOLESTEROL × 4 1PE PENTAETHYLENE GLYCOL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 11 92S 1-(4-fluorophenyl)-4-[(10~{R},15~{S})-4-methyl-1,4,12-triazatetracyclo[7.6.1.0^{5,16}.0^{10,15}]hexadeca-5,7,9(16)-trien-12-yl]butan-1-one × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 8；293.15 K；100 mM Tris-HCl, 160 mM Potassium fluoride, 30% (v/v) PEG400
Resolution 2.45 Å R-free 0.244
7WC9 Crystal structure of serotonin 2A receptor in complex with non-hallucinogenic psychedelic analog Deposited 2021-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 67–265（199 aa）
Chain A 313–403（91 aa）
Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N MG MAGNESIUM ION × 1 CLR CHOLESTEROL × 3 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 93F (10~{R},15~{S})-12-[3-(2-methoxyphenyl)propyl]-4-methyl-1,4,12-triazatetracyclo[7.6.1.0^{5,16}.0^{10,15}]hexadeca-5(16),6,8-triene × 1 1PE PENTAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Tris-HCl, 40 mM sodium acetate trihydrate, 30% (v/v) PEG400, 2% (v/v) Polypropylene glycol P 400
Resolution 2.50 Å R-free 0.266
8JT8 Crystal structure of 5-HT2AR in complex with (R)-IHCH-7179 Deposited 2023-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–265（196 aa）
Chain A 313–403（91 aa）
Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N Mutation：S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N MG MAGNESIUM ION × 1 EZX 1-(4-fluorophenyl)-4-[(7R)-2,5,11-triazatetracyclo[7.6.1.0^2,7.0^12,16]hexadeca-1(15),9,12(16),13-tetraen-5-yl]butan-1-one × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 7 CLR CHOLESTEROL × 2 1PE PENTAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 8；293.15 K；100 mM Tris/HCl, 160 mM Potassium fluoride, 30% PEG400
Resolution 2.70 Å R-free 0.270
8UWL 5-HT2AR bound to Lisuride in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM) Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 66–404（339 aa）
Not recorded H8G N,N-diethyl-N'-[(8alpha)-6-methyl-9,10-didehydroergolin-8-yl]urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8V6U 5HT2AR-miniGq heterotrimer in complex with a novel agonist obtained from large scale docking Deposited 2023-12-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 66–404（339 aa）
Not recorded YEQ 4-{(3R)-1-[(1R)-1-(pyrimidin-2-yl)ethyl]piperidin-3-yl}phenol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
8ZMG Crystal structure of an inverse agonist antipsychotic drug pimavanserin-bound 5-HT2A Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 70–265（196 aa）
Chain A 313–403（91 aa）
Mutation：S162K,M164W,M29W,H124I,R128L,R315G Mutation：S162K,M164W,M29W,H124I,R128L,R315G A1L11 Pimavanserin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；32-38%PEG300, 40-60mM lithium chloride
Resolution 3.40 Å R-free 0.328
8ZMG Crystal structure of an inverse agonist antipsychotic drug pimavanserin-bound 5-HT2A Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 70–265（196 aa）
Chain B 313–403（91 aa）
Mutation：S162K,M164W,M29W,H124I,R128L,R315G Mutation：S162K,M164W,M29W,H124I,R128L,R315G A1L11 Pimavanserin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；32-38%PEG300, 40-60mM lithium chloride
Resolution 3.40 Å R-free 0.328
9ARX Local refinement of 5-HT2AR bound to 5-HT in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–471（471 aa）
Not recorded SRO SEROTONIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.24 Å
9ARY Global reconstruction 5-HT2AR bound to 5-HT in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–471（471 aa）
Not recorded SRO SEROTONIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
9ARZ Local refinement of 5-HT2AR bound to 2-bromo-LSD in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–471（471 aa）
Not recorded A1AFU 2-bromo-N,N-diethyl-6-methyl-9,10-didehydroergoline-8beta-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.37 Å
9AS0 Global reconstruction of 5-HT2AR bound to 2-bromo-LSD in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–471（471 aa）
Not recorded A1AFU 2-bromo-N,N-diethyl-6-methyl-9,10-didehydroergoline-8beta-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.38 Å
9AS1 Local refinement of 5-HT2AR bound to DMT in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–471（471 aa）
Not recorded A1AFV 2-(1H-indol-3-yl)-N,N-dimethylethan-1-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.38 Å
9AS2 Global reconstruction of 5-HT2AR bound to DMT in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–471（471 aa）
Not recorded A1AFV 2-(1H-indol-3-yl)-N,N-dimethylethan-1-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.21 Å
9AS3 Local refinement of 5-HT2AR bound to LSD in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–471（471 aa）
Not recorded 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.18 Å
9AS4 Global reconstruction of 5-HT2AR bound to LSD in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–471（471 aa）
Not recorded 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.06 Å
9AS5 Local refinement of 5-HT2AR bound to Mescaline in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–471（471 aa）
Not recorded A1AFW Mescaline × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.34 Å
9AS6 Global reconstruction of 5-HT2AR bound to mescaline in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–471（471 aa）
Not recorded A1AFW Mescaline × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.07 Å
9AS7 Local refinement of 5-HT2AR bound to psilocin in complex with a mini-Gq and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–471（471 aa）
Not recorded 91Q 3-[2-(dimethylamino)ethyl]-1~{H}-indol-4-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.72 Å
9AS8 Global reconstruction of 5-HT2AR bound to psilocin in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–471（471 aa）
Not recorded 91Q 3-[2-(dimethylamino)ethyl]-1~{H}-indol-4-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.54 Å
9ASA Global reconstruction of 5-HT2AR bound to RS130-180 in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM) Deposited 2024-02-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–471（471 aa）
Not recorded A1AFX 2,5-dimethoxy-N,N-dimethyl-4-{2-[({2-[(prop-2-yn-1-yl)oxy]phenyl}methyl)amino]ethyl}aniline × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.12 Å
9J87 Structure of Receptor Deposited 2024-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 66–404（339 aa）
Not recorded F5U 2-(5-methoxy-1H-indol-3-yl)ethanamine × 1 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
9LL7 DOI-bound Serotonin 2A (5-HT2A) receptor-Gi complex Deposited 2025-01-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–471（471 aa）
Not recorded CLR CHOLESTEROL × 1 A1EK5 (2~{R})-1-(4-iodanyl-2,5-dimethoxy-phenyl)propan-2-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
9LL8 Psilocin-bound Serotonin 2A (5-HT2A) receptor-Gi complex Deposited 2025-01-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–471（471 aa）
Not recorded 91Q 3-[2-(dimethylamino)ethyl]-1~{H}-indol-4-ol × 1 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
9LL9 DOI-bound Serotonin 2A (5-HT2A) receptor-Gq complex Deposited 2025-01-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–471（471 aa）
Not recorded A1EK5 (2~{R})-1-(4-iodanyl-2,5-dimethoxy-phenyl)propan-2-amine × 1 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
9LLA Ariadne-bound Serotonin 2A (5-HT2A) receptor-Gq complex Deposited 2025-01-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–471（471 aa）
Not recorded A1EK8 (2~{R})-1-(2,5-dimethoxy-4-methyl-phenyl)butan-2-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
9LLB DOI-NBOMe-bound Serotonin 2A (5-HT2A) receptor-Gq complex Deposited 2025-01-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–471（471 aa）
Not recorded CLR CHOLESTEROL × 1 A1ELA (2~{R})-1-(4-iodanyl-2,5-dimethoxy-phenyl)-~{N}-[(2-methoxyphenyl)methyl]propan-2-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9UJM Structure of a membrane protein Deposited 2025-04-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 66–405（340 aa）
Not recorded A1L11 Pimavanserin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å

38 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 5HT2A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–471； UniProt 1–471

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9as9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9as9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9as9
Deposition date deposition_date2024-02-24
Structure title titleLocal refinement of 5-HT2AR bound to RS130-180 in complex with a mini-Gq protein and scFv16 obtained by cryo-electron microscopy (cryoEM)
Keywords keywordsGPCR, G-protein Coupled Receptor, 5-HT2AR, serotonin, psychedelics, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.27 Å
Radius of gyration Rg (electron density) rg_electron19.27 Å
Forward intensity I(0) i022919100.00
Molecular weight molecular_weight25813.0 kDa
Excluded volume excluded_volume25754 ų
Envelope volume envelope_volume42350 ų
Hydration-shell volume shell_volume18759 ų
Envelope diameter envelope_diameter67.8 Å
Shell Rg shell_rg25.20 Å
Envelope Rg envelope_rg19.60 Å
Shape Rg shape_rg19.24 Å
Total Rg total_rg20.03 Å
Total atoms total_atoms1965
Residues n_residues261
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax64.6 Å
Rg (real space) rg_real20.25 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real2.2920e+07
I(0) uncertainty (real space) i0_real_error3.0680e+05
Rg (reciprocal space) rg_reciprocal20.26 Å
I(0) (reciprocal space) i0_reciprocal22920000.0000
Solution quality estimate total_estimate0.7320
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.0 Å
Skewness Skewness skewness0.341
Kurtosis Kurtosis kurtosis-0.332
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2346000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 0.319; Positv: 1.000; Valcen: 1.000; Smooth: 0.902
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)