Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.14 kDa 
• Atom Count: 3655 
• Modelled Residue Count: 392 
• Deposited Residue Count: 442 
• Unique protein chains: 1

6PS7

XFEL A2aR structure by ligand exchange from LUF5843 to ZM241385.

• DOI: 10.2210/pdb6PS7/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2019-07-12 Released: 2019-11-13 
• Deposition Author(s): Ishchenko, A., Stauch, B., Han, G.W., Batyuk, A., Shiriaeva, A., Li, C., Zatsepin, N.A., Weierstall, U., Liu, W., Nango, E., Nakane, T., Tanaka, R., Tono, K., Joti, Y., Iwata, S., Moraes, I., Gati, C., Cherezov, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.201 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Toward G protein-coupled receptor structure-based drug design using X-ray lasers.

Ishchenko, A., Stauch, B., Han, G.W., Batyuk, A., Shiriaeva, A., Li, C., Zatsepin, N., Weierstall, U., Liu, W., Nango, E., Nakane, T., Tanaka, R., Tono, K., Joti, Y., Iwata, S., Moraes, I., Gati, C., Cherezov, V.

(2019) IUCrJ 6: 1106-1119

• PubMed: 31709066 
• DOI: 10.1107/S2052252519013137
• Primary Citation of Related Structures:  
  6PS2, 6PS1, 6PS4, 6PS3, 6PS6, 6PS5, 6PS8, 6PS7, 6PS0, 6PRZ


• PubMed Abstract: 
  

Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β ₂ -adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.

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Organizational Affiliation: 

Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a	A	442	Homo sapiens, Escherichia coli	Mutation(s): 3  Gene Names: ADORA2A, ADORA2, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens) Explore P29274  Go to UniProtKB:  P29274
PHAROS:  P29274 GTEx:  ENSG00000128271

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR (Subject of Investigation/LOI)	L [auth A], M [auth A], N [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLB (Subject of Investigation/LOI)	O [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-QJRAZLAKSA-N
OLC (Subject of Investigation/LOI)	C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
ZMA (Subject of Investigation/LOI)	B [auth A]	4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol C16 H15 N7 O2 PWTBZOIUWZOPFT-UHFFFAOYSA-N
OLA (Subject of Investigation/LOI)	AA [auth A],  BA [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  X [auth A],  Y [auth A],  Z [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NA	CA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMA	BindingDB:  6PS7	Ki: min: 0.1, max: 64 (nM) from 16 assay(s)
		Kd: 0.22 (nM) from 1 assay(s)
		IC50: min: 0.68, max: 81 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.201 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.32	α = 90
b = 180.49	β = 90
c = 142.48	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-07-12 
• Released Date: 2019-11-13 
Deposition Author(s): Ishchenko, A., Stauch, B., Han, G.W., Batyuk, A., Shiriaeva, A., Li, C., Zatsepin, N.A., Weierstall, U., Liu, W., Nango, E., Nakane, T., Tanaka, R., Tono, K., Joti, Y., Iwata, S., Moraes, I., Gati, C., Cherezov, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM127086

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence