6MXT | pdb_00006mxt

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 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6MXT

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41589-018-0145-x
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 68.73 kDa 
  • Atom Count: 4,683 
  • Modeled Residue Count: 571 
  • Deposited Residue Count: 594 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endolysin, Beta-2 adrenergic receptor chimera472Tequatrovirus T4Homo sapiensMutation(s): 3 
Gene Names: eT4Tp126ADRB2ADRB2RB2AR
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
PHAROS:  P07550
GTEx:  ENSG00000169252 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P07550
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
nanobody Nb71B [auth N]122Lama glamaMutation(s): 0 

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K5Y
(Subject of Investigation/LOI)

Query on K5Y



Download:Ideal Coordinates CCD File
C [auth A]salmeterol
C25 H37 N O4
GIIZNNXWQWCKIB-VWLOTQADSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
F [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
P33

Query on P33



Download:Ideal Coordinates CCD File
I [auth A]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
OLA

Query on OLA



Download:Ideal Coordinates CCD File
H [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
HTO

Query on HTO



Download:Ideal Coordinates CCD File
G [auth A]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
E [auth A],
J [auth N],
K [auth N]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
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

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary