Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.86 kDa 
• Atom Count: 3628 
• Residue Count: 442 
• Unique protein chains: 1

3PDS

Irreversible Agonist-Beta2 Adrenoceptor Complex

• DOI: 10.2210/pdb3PDS/pdb

• Classification: Membrane Protein/Hydrolase
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-10-24 Released: 2011-01-12 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.283 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 

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

• PubMed: 21228876 
• DOI: 10.1038/nature09665
• Primary Citation of Related Structures:  
  3PDS


• 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, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein Beta-2 adrenergic receptor/Lysozyme	A	458	Homo sapiens, Escherichia virus T4	Mutation(s): 3  Gene Names: ADRB2, ADRB2R, B2AR EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  β2 adrenergic receptor (engineered) with irreversibly-bound agonist
Find proteins for P07550 (Homo sapiens) Explore P07550  Go to UniProtKB:  P07550
NIH Common Fund Data Resources
PHAROS  P07550 GTEx  ENSG00000169252
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ERC	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
CLR	A	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.283 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 282.44	α = 90
b = 40.04	β = 90
c = 65.21	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-24 
• Released Date: 2011-01-12 
Deposition Author(s): 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.

Revision History 

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