7SRS | pdb_00007srs

5-HT2B receptor bound to LSD in complex with beta-arrestin1 obtained by cryo-electron microscopy (cryoEM)

• PDB DOI: https://doi.org/10.2210/pdb7SRS/pdb
• EM Map EMD-25403: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2021-11-08 Released: 2022-09-21 
• Deposition Author(s): Barros-Alvarez, X., Cao, C., Panova, O., Roth, B.L., Skiniotis, G.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Signaling snapshots of a serotonin receptor activated by the prototypical psychedelic LSD.

Cao, C., Barros-Alvarez, X., Zhang, S., Kim, K., Damgen, M.A., Panova, O., Suomivuori, C.M., Fay, J.F., Zhong, X., Krumm, B.E., Gumpper, R.H., Seven, A.B., Robertson, M.J., Krogan, N.J., Huttenhain, R., Nichols, D.E., Dror, R.O., Skiniotis, G., Roth, B.L.

(2022) Neuron 110: 3154

• PubMed: 36087581 
• DOI: https://doi.org/10.1016/j.neuron.2022.08.006
• Primary Citation of Related Structures:  
  7SRQ, 7SRR, 7SRS


• PubMed Abstract: 
  

  Serotonin (5-hydroxytryptamine [5-HT]) 5-HT2-family receptors represent essential targets for lysergic acid diethylamide (LSD) and all other psychedelic drugs. Although the primary psychedelic drug effects are mediated by the 5-HT _2A serotonin receptor (HTR2A), the 5-HT _2B serotonin receptor (HTR2B) has been used as a model receptor to study the activation mechanisms of psychedelic drugs due to its high expression and similarity to HTR2A. In this study, we determined the cryo-EM structures of LSD-bound HTR2B in the transducer-free, Gq-protein-coupled, and β-arrestin-1-coupled states. These structures provide distinct signaling snapshots of LSD's action, ranging from the transducer-free, partially active state to the transducer-coupled, fully active states. Insights from this study will both provide comprehensive molecular insights into the signaling mechanisms of the prototypical psychedelic LSD and accelerate the discovery of novel psychedelic drugs.

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Organizational Affiliation: 
• Department of Pharmacology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599-7365, USA.
Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 7599-7365, USA.
Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; J. David Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7365, USA.
Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA. Electronic address: [e-mail].
Department of Molecular and Cellular Physiology, Department of Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA. Electronic address: [e-mail].
Department of Pharmacology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599-7365, USA; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599-7365, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 150.38 kDa 
• Atom Count: 8,361 
• Modeled Residue Count: 1,103 
• Deposited Residue Count: 1,352 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-5HT2BR Fab light chain	A [auth P]	209	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-5HT2BR Fab heavy chain	B [auth Q]	218	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2B	C [auth R]	333	Homo sapiens	Mutation(s): 0  Gene Names: HTR2B Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41595 (Homo sapiens) Explore P41595  Go to UniProtKB:  P41595
PHAROS:  P41595 GTEx:  ENSG00000135914
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P41595-1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1B of Beta-arrestin-1	D [auth C]	367	Homo sapiens	Mutation(s): 1  Gene Names: ARRB1, ARR1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens) Explore P49407  Go to UniProtKB:  P49407
PHAROS:  P49407 GTEx:  ENSG00000137486

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab30 heavy chain	E [auth H]	119	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab30 light chain	F [auth L]	106	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7LD (Subject of Investigation/LOI)	H [auth R]	(8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide C20 H25 N3 O VAYOSLLFUXYJDT-RDTXWAMCSA-N
NAG	G [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C [auth R]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
7LD	BindingDB:  7SRS	Ki: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Barros-Alvarez, X., Cao, C., Panova, O., Roth, B.L., Skiniotis, G.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2022-10-05
  Changes: Structure summary
• Version 1.2: 2022-10-19
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Data collection, Structure summary