6N48 | pdb_00006n48

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

• PDB DOI: https://doi.org/10.2210/pdb6N48/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Enterobacteria phage RB59, Homo sapiens, Camelidae
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2018-11-17 Released: 2019-06-26 
• Deposition Author(s): Liu, X., Masoudi, A., Kahsai, A.W., Huang, L.Y., Pani, B., Hirata, K., Ahn, S., Lefkowitz, R.J., Kobilka, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.274 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

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

• PubMed: 31249059 
• DOI: https://doi.org/10.1126/science.aaw8981
• Primary Citation Related Structures: 
  6N48


• 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 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.

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Organizational Affiliation: 
• 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.
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.
Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA. [e-mail] [e-mail].
Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.
Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. [e-mail] [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.76 kDa 
• Atom Count: 4,585 
• Modeled Residue Count: 574 
• Deposited Residue Count: 589 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin,Beta-2 adrenergic receptor,Beta-2 adrenergic receptor chimera	A	469	Enterobacteria phage RB59, Homo sapiens	Mutation(s): 6  Gene Names: e, RB59_126, ADRB2, ADRB2R, B2AR EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens) Explore P07550  Go to UniProtKB:  P07550
PHAROS:  P07550 GTEx:  ENSG00000169252

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Camelid Antibody Fragment	B	120	Camelidae	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KBY	E [auth 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
P0G	C [auth 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
1WV	D [auth A]	(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate C17 H32 O4 LVBAGTJIDOCNIJ-INIZCTEOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P0G	BindingDB:  6N48	EC50: 0.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.274 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.15	α = 90
b = 66.06	β = 90
c = 303.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Liu, X., Masoudi, A., Kahsai, A.W., Huang, L.Y., Pani, B., Hirata, K., Ahn, S., Lefkowitz, R.J., Kobilka, B.K.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 1.2: 2019-07-10
  Changes: Data collection, Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary