5TVN

Crystal structure of the LSD-bound 5-HT2B receptor


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • 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 s ...

    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.


    Organizational Affiliation

    Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA. Electronic address: dwacker@email.unc.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562
A
402Escherichia coliHomo sapiens
This entity is chimeric
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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
7LD
Query on 7LD

Download SDF File 
Download CCD File 
A
(8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide
C20 H25 N3 O
VAYOSLLFUXYJDT-RDTXWAMCSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
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 = 59.195α = 90.00
b = 119.177β = 90.00
c = 170.990γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of Mental HealthUnited StatesPsychoactive Drug Screening Program (PDSP)
National Institutes of Health/National Institute of Mental HealthUnited StatesU19MH82441

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