6DRY

Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural determinants of 5-HT2Breceptor activation and biased agonism.

McCorvy, J.D., Wacker, D., Wang, S., Agegnehu, B., Liu, J., Lansu, K., Tribo, A.R., Olsen, R.H.J., Che, T., Jin, J., Roth, B.L.

(2018) Nat Struct Mol Biol 25: 787-796

  • DOI: 10.1038/s41594-018-0116-7
  • Primary Citation of Related Structures:  
    6DRY, 6DRX, 6DRZ, 6DS0

  • PubMed Abstract: 

    • Serotonin (5-hydroxytryptamine; 5-HT) receptors modulate a variety of physiological processes ranging from perception, cognition and emotion to vascular and smooth muscle contraction, platelet aggregation, gastrointestinal function and reproduction. ...

    Serotonin (5-hydroxytryptamine; 5-HT) receptors modulate a variety of physiological processes ranging from perception, cognition and emotion to vascular and smooth muscle contraction, platelet aggregation, gastrointestinal function and reproduction. Drugs that interact with 5-HT receptors effectively treat diseases as diverse as migraine headaches, depression and obesity. Here we present four structures of a prototypical serotonin receptor-the human 5-HT 2B receptor-in complex with chemically and pharmacologically diverse drugs, including methysergide, methylergonovine, lisuride and LY266097. A detailed analysis of these structures complemented by comprehensive interrogation of signaling illuminated key structural determinants essential for activation. Additional structure-guided mutagenesis experiments revealed binding pocket residues that were essential for agonist-mediated biased signaling and β-arrestin2 translocation. Given the importance of 5-HT receptors for a large number of therapeutic indications, insights derived from these studies should accelerate the design of safer and more effective medications.

    Organizational Affiliation: 

    National Institute of Mental Health Psychoactive Drug Screening Program, Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, USA. bryan_roth@med.unc.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5HT2B receptor, BRIL chimeraA411Homo sapiens, Escherichia coliMutation(s): 2 
Gene Names: HTR2B
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A		Protein: 
5-HT2B serotonin receptor with bound methylergonovine
Find proteins for P41595 (Homo sapiens)
Explore P41595 
Go to UniProtKB:  P41595
NIH Common Fund Data Resources
PHAROS  P41595
GTEx  ENSG00000135914
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR
Download Ideal Coordinates CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N		 Ligand Interaction
OLC
Query on OLC
Download Ideal Coordinates CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N		 Ligand Interaction
H8D
Query on H8D
Download Ideal Coordinates CCD File 
A
(8beta)-N-[(2S)-1-hydroxybutan-2-yl]-6-methyl-9,10-didehydroergoline-8-carboxamide
C20 H25 N3 O2
UNBRKDKAWYKMIV-QWQRMKEZSA-N		 Ligand Interaction
OLA
Query on OLA
Download Ideal Coordinates CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.662α = 90
b = 119.452β = 90
c = 171.021γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesRO1MH61887
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesU19MH82441
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01NS100930
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAGM-12006
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence