3PDS

Irreversible Agonist-Beta2 Adrenoceptor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and function of an irreversible agonist-beta(2) adrenoceptor complex

Rosenbaum, D.M.Zhang, C.Lyons, J.A.Holl, R.Aragao, D.Arlow, D.H.Rasmussen, S.G.F.Choi, H.J.Devree, B.T.Sunahara, R.K.Chae, P.S.Gellman, S.H.Dror, R.O.Shaw, D.E.Weis, W.I.Caffrey, M.Gmeiner, P.Kobilka, B.K.

(2011) Nature 469: 236-240

  • DOI: 10.1038/nature09665

  • PubMed Abstract: 
  • G-protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that modulate biological function by initiating cellular signalling in response to chemically diverse agonists. Despite recent progress in the structural biology of GPCRs, ...

    G-protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that modulate biological function by initiating cellular signalling in response to chemically diverse agonists. Despite recent progress in the structural biology of GPCRs, the molecular basis for agonist binding and allosteric modulation of these proteins is poorly understood. Structural knowledge of agonist-bound states is essential for deciphering the mechanism of receptor activation, and for structure-guided design and optimization of ligands. However, the crystallization of agonist-bound GPCRs has been hampered by modest affinities and rapid off-rates of available agonists. Using the inactive structure of the human β(2) adrenergic receptor (β(2)AR) as a guide, we designed a β(2)AR agonist that can be covalently tethered to a specific site on the receptor through a disulphide bond. The covalent β(2)AR-agonist complex forms efficiently, and is capable of activating a heterotrimeric G protein. We crystallized a covalent agonist-bound β(2)AR-T4L fusion protein in lipid bilayers through the use of the lipidic mesophase method, and determined its structure at 3.5 Å resolution. A comparison to the inactive structure and an antibody-stabilized active structure (companion paper) shows how binding events at both the extracellular and intracellular surfaces are required to stabilize an active conformation of the receptor. The structures are in agreement with long-timescale (up to 30 μs) molecular dynamics simulations showing that an agonist-bound active conformation spontaneously relaxes to an inactive-like conformation in the absence of a G protein or stabilizing antibody.


    Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion protein Beta-2 adrenergic receptor/Lysozyme
A
458Enterobacteria phage T4Homo sapiens
This entity is chimeric
Gene Names: E, ADRB2 (ADRB2R, B2AR)
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
β2 adrenergic receptor
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ERC
Query on ERC

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Download CCD File 
A
8-hydroxy-5-[(1R)-1-hydroxy-2-({2-[3-methoxy-4-(3-sulfanylpropoxy)phenyl]ethyl}amino)ethyl]quinolin-2(1H)-one
C23 H28 N2 O5 S
WAQRESHSGHIXBV-IBGZPJMESA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 282.440α = 90.00
b = 40.040β = 90.00
c = 65.210γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
JBluIce-EPICSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy