6MXT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    6MXT

  • PubMed Abstract: 
  • 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. 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

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endolysin, Beta-2 adrenergic receptor chimeraA472Escherichia virus T4Homo sapiensMutation(s): 3 
Gene Names: ET4Tp126
EC: 3.2.1.17
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
NIH Common Fund Data Resources
PHAROS  P07550
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
nanobody Nb71N122Lama glamaMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K5Y
Query on K5Y

Download Ideal Coordinates CCD File 
A
salmeterol
C25 H37 N O4
GIIZNNXWQWCKIB-VWLOTQADSA-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
P33
Query on P33

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

Download Ideal Coordinates CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
HTO
Query on HTO

Download Ideal Coordinates CCD File 
A
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
A, N
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
AL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.682α = 90
b = 52.589β = 123.859
c = 125.917γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
PHASERphasing
Cootmodel building
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5U19GM106990-05
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM128641-01

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence