5TVN

Crystal structure of the LSD-bound 5-HT2B receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.7 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: https://doi.org/10.1016/j.cell.2016.12.033
  • Primary Citation of Related Structures:  
    5TVN

  • 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-HT 2B . 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-HT 2B R and 5-HT 2A R-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562402Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: HTR2BcybC
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 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P41595
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
7LD
Query on 7LD

Download Ideal Coordinates CCD File 
B [auth A](8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide
C20 H25 N3 O
VAYOSLLFUXYJDT-RDTXWAMCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.195α = 90
b = 119.177β = 90
c = 170.99γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesPsychoactive Drug Screening Program (PDSP)
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesU19MH82441

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Data collection
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Refinement description
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2022-10-05
    Changes: Database references, Structure summary
  • Version 1.6: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.7: 2024-11-13
    Changes: Structure summary