6N48

Structure of beta2 adrenergic receptor bound to BI167107, Nanobody 6B9, and a positive allosteric modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of beta2AR regulation by an intracellular positive allosteric modulator.

Liu, X.Masoudi, A.Kahsai, A.W.Huang, L.Y.Pani, B.Staus, D.P.Shim, P.J.Hirata, K.Simhal, R.K.Schwalb, A.M.Rambarat, P.K.Ahn, S.Lefkowitz, R.J.Kobilka, B.

(2019) Science 364: 1283-1287

  • DOI: 10.1126/science.aaw8981

  • PubMed Abstract: 
  • Drugs targeting the orthosteric, primary binding site of G protein-coupled receptors are the most common therapeutics. Allosteric binding sites, elsewhere on the receptors, are less well-defined, and so less exploited clinically. We report the crysta ...

    Drugs targeting the orthosteric, primary binding site of G protein-coupled receptors are the most common therapeutics. Allosteric binding sites, elsewhere on the receptors, are less well-defined, and so less exploited clinically. We report the crystal structure of the prototypic β 2 -adrenergic receptor in complex with an orthosteric agonist and compound-6FA, a positive allosteric modulator of this receptor. It binds on the receptor's inner surface in a pocket created by intracellular loop 2 and transmembrane segments 3 and 4, stabilizing the loop in an α-helical conformation required to engage the G protein. Structural comparison explains the selectivity of the compound for β 2 - over the β 1 -adrenergic receptor. Diversity in location, mechanism, and selectivity of allosteric ligands provides potential to expand the range of receptor drugs.


    Organizational Affiliation

    Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo 679-5148, Japan.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. lefko001@receptor-biol.duke.edu kobilka@stanford.edu.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA. lefko001@receptor-biol.duke.edu kobilka@stanford.edu.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.,Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin,Beta-2 adrenergic receptor,Beta-2 adrenergic receptor chimera
A
469Homo sapiensEnterobacteria phage RB59
This entity is chimeric
Mutation(s): 6 
Gene Names: ADRB2 (ADRB2R, B2AR), e
EC: 3.2.1.17
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
β2 adrenergic receptor
Find proteins for P07550 (Homo sapiens)
Go to Gene View: ADRB2
Go to UniProtKB:  P07550
Find proteins for A0A097J809 (Enterobacteria phage RB59)
Go to UniProtKB:  A0A097J809
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Camelid Antibody Fragment
B
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KBY
Query on KBY

Download SDF File 
Download CCD File 
A
N-[(3R)-4-(4-tert-butylphenyl)-3-({2-[(4-methoxyphenyl)sulfanyl]-5-[methyl(propan-2-yl)sulfamoyl]benzene-1-carbonyl}amino)butanoyl]glycine
C34 H43 N3 O7 S2
POBZRCRFILRWTQ-RUZDIDTESA-N
 Ligand Interaction
P0G
Query on P0G

Download SDF File 
Download CCD File 
A
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
C21 H26 N2 O4
NWQXBEWHTDRJIP-KRWDZBQOSA-N
 Ligand Interaction
1WV
Query on 1WV

Download SDF File 
Download CCD File 
A
(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate
C17 H32 O4
LVBAGTJIDOCNIJ-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.150α = 90.00
b = 66.060β = 90.00
c = 303.510γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Type: Data collection, Database references
  • Version 1.2: 2019-07-10
    Type: Data collection, Database references