Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46500.73 
• Atom Count: 3022 
• Residue Count: 402 
• Unique protein chains: 1

5TVN

Crystal structure of the LSD-bound 5-HT2B receptor

• DOI: 10.2210/pdb5TVN/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): 4 


• Deposited: 2016-11-09 Released: 2017-02-01 
• Deposition Author(s): Wacker, D., Wang, S., McCorvy, J.D., Betz, R.M., Venkatakrishnan, A.J., Levit, A., Lansu, K., Schools, Z.L., Che, T., Nichols, D.E., Shoichet, B.K., Dror, R.O., Roth, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.263 
• R-Value Work: 0.210 

Literature

Crystal Structure of an LSD-Bound Human Serotonin Receptor.

Wacker, D., Wang, S., McCorvy, J.D., Betz, R.M., Venkatakrishnan, A.J., Levit, A., Lansu, K., Schools, Z.L., Che, T., Nichols, D.E., Shoichet, B.K., Dror, R.O., Roth, B.L.

(2017) Cell 168: 377-389.e12

• PubMed: 28129538 
• DOI: 10.1016/j.cell.2016.12.033


• PubMed Abstract: 
  

The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR-a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors. PAPERCLIP.

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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. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562	A	402	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 4  Gene Names: cybC, HTR2B
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs)	Protein:  5-HT2B serotonin receptor with bound ergotamine
Find proteins for P0ABE7 (Escherichia coli) Go to UniProtKB:  P0ABE7
Find proteins for P41595 (Homo sapiens) Go to Gene View: HTR2B Go to UniProtKB:  P41595

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLC	A	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
7LD	A	(8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide C20 H25 N3 O VAYOSLLFUXYJDT-RDTXWAMCSA-N
CLR	A	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.263 
• R-Value Work: 0.210 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 59.195	α = 90.00
b = 119.177	β = 90.00
c = 170.990	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-11-09 
• Released Date: 2017-02-01 
• Deposition Author(s): Wacker, D., Wang, S., McCorvy, J.D., Betz, R.M., Venkatakrishnan, A.J., Levit, A., Lansu, K., Schools, Z.L., Che, T., Nichols, D.E., Shoichet, B.K., Dror, R.O., Roth, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health	United States	Psychoactive Drug Screening Program (PDSP)
National Institutes of Health/National Institute of Mental Health	United States	U19MH82441

Revision History 

• Version 1.0: 2017-02-01
  Type: Initial release
• Version 1.1: 2017-02-08
  Type: Database references
• Version 1.2: 2017-02-22
  Type: Data collection
• Version 1.3: 2017-09-27
  Type: Author supporting evidence, Refinement description