6MXT

Crystal structure of human beta2 adrenergic receptor bound to salmeterol and Nb71


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95934 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into binding specificity, efficacy and bias of a beta2AR partial agonist.

Masureel, M.Zou, Y.Picard, L.P.van der Westhuizen, E.Mahoney, J.P.Rodrigues, J.P.G.L.M.Mildorf, T.J.Dror, R.O.Shaw, D.E.Bouvier, M.Pardon, E.Steyaert, J.Sunahara, R.K.Weis, W.I.Zhang, C.Kobilka, B.K.

(2018) Nat. Chem. Biol. 14: 1059-1066

  • DOI: 10.1038/s41589-018-0145-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Salmeterol is a partial agonist for the β <sub>2 </sub> adrenergic receptor (β <sub>2 </sub>AR) and the first long-acting β <sub>2 </sub>AR agonist to be widely used clinically for the treatment of asthma and chronic obstructive pulmonary disease. Sa ...

    Salmeterol is a partial agonist for the β 2 adrenergic receptor (β 2 AR) and the first long-acting β 2 AR agonist to be widely used clinically for the treatment of asthma and chronic obstructive pulmonary disease. Salmeterol's safety and mechanism of action have both been controversial. To understand its unusual pharmacological action and partial agonism, we obtained the crystal structure of salmeterol-bound β 2 AR in complex with an active-state-stabilizing nanobody. The structure reveals the location of the salmeterol exosite, where sequence differences between β 1 AR and β 2 AR explain the high receptor-subtype selectivity. A structural comparison with the β 2 AR bound to the full agonist epinephrine reveals differences in the hydrogen-bond network involving residues Ser204 5.43 and Asn293 6.55 . Mutagenesis and biophysical studies suggested that these interactions lead to a distinct active-state conformation that is responsible for the partial efficacy of G-protein activation and the limited β-arrestin recruitment for salmeterol.


    Organizational Affiliation

    D. E. Shaw Research, New York, NY, USA.,Geneus Technologies, Ltd, Chengdu, Sichuan, People's Republic of China.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. chengzh@pitt.edu.,Dropbox, New York, NY, USA.,Structural Biology Research Center, VIB, Brussels, Belgium.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Monash Institute for Pharmaceutical Sciences, Monash University, Victoria, Australia.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Department of Biochemistry, Institute for Research in Immunology and Cancer, Université de Montreal, Montreal, Québec, Canada.,Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Computer Science and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin, Beta-2 adrenergic receptor chimera
A
472Enterobacteria phage T4Homo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: E, ADRB2 (ADRB2R, B2AR)
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for P07550 (Homo sapiens)
Go to Gene View: ADRB2
Go to UniProtKB:  P07550
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
nanobody Nb71
N
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
K5Y
Query on K5Y

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A
salmeterol
2-(hydroxymethyl)-4-[(1R)-1-hydroxy-2-{[6-(4-phenylbutoxy)hexyl]amino}ethyl]phenol
C25 H37 N O4
GIIZNNXWQWCKIB-VWLOTQADSA-N
 Ligand Interaction
P33
Query on P33

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Download CCD File 
A
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
HEPTAETHYLENE GLYCOL, PEG330
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

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A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

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A
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
NI
Query on NI

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A, N
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95934 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 178.682α = 90.00
b = 52.589β = 123.86
c = 125.917γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States5U19GM106990-05
National Institutes of Health/National Institute of General Medical SciencesUnited States1R35GM128641-01

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release