5TVN | pdb_00005tvn

Crystal structure of the LSD-bound 5-HT2B receptor

• PDB DOI: https://doi.org/10.2210/pdb5TVN/pdb

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


• 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 (NIH/NIMH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.263 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.cell.2016.12.033
• Primary Citation 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.

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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].
Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA.
Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158-2280, USA.
Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA.
Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, 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 at Chapel Hill, Chapel Hill, NC 27599-7360, USA; National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.5 kDa 
• Atom Count: 3,023 
• Modeled Residue Count: 393 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562	A	402	Homo sapiens, Escherichia coli	Mutation(s): 4  Gene Names: HTR2B, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P41595 (Homo sapiens) Explore P41595  Go to UniProtKB:  P41595
PHAROS:  P41595 GTEx:  ENSG00000135914
UniProt Groups	P0ABE7P41595

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	C [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC	D [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
7LD	B [auth A]	(8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide C20 H25 N3 O VAYOSLLFUXYJDT-RDTXWAMCSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	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 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.195	α = 90
b = 119.177	β = 90
c = 170.99	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• 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 (NIH/NIMH)	United States	Psychoactive Drug Screening Program (PDSP)
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	U19MH82441

Revision History  

• 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