6JZH

Structure of human A2A adenosine receptor in complex with ZM241385 obtained from SFX experiments under atmospheric pressure

• PDB DOI: https://doi.org/10.2210/pdb6JZH/pdb

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


• Deposited: 2019-05-02 Released: 2019-10-30 
• Deposition Author(s): Nango, E., Shimamura, T., Nakane, T., Yamanaka, Y., Mori, C., Kimura, K.T., Fujiwara, T., Tanaka, T., Iwata, S.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure.

Shimazu, Y., Tono, K., Tanaka, T., Yamanaka, Y., Nakane, T., Mori, C., Terakado Kimura, K., Fujiwara, T., Sugahara, M., Tanaka, R., Doak, R.B., Shimamura, T., Iwata, S., Nango, E., Yabashi, M.

(2019) J Appl Crystallogr 52: 1280-1288

• PubMed: 31798359 
• DOI: https://doi.org/10.1107/S1600576719012846
• Primary Citation of Related Structures:  
  6JZH, 6JZI


• PubMed Abstract: 
  

  A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A _2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump-probe techniques.

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Organizational Affiliation: 

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.88 kDa 
• Atom Count: 3,373 
• Modelled Residue Count: 390 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a	A	447	Homo sapiens, Escherichia coli	Mutation(s): 4  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
UniProt Groups	P0ABE7P29274

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	W [auth A], X [auth A], Y [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
ZMA	C [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	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMA	BindingDB:  6JZH	Ki: min: 0.1, max: 395 (nM) from 18 assay(s)
		Kd: min: 0.22, max: 286 (nM) from 2 assay(s)
		IC50: min: 0.68, max: 81 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.11577/1572697
• Diffraction Data: https://doi.org/10.11577/1572698

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.17	α = 90
b = 179.59	β = 90
c = 142.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Nango, E., Shimamura, T., Nakane, T., Yamanaka, Y., Mori, C., Kimura, K.T., Fujiwara, T., Tanaka, T., Iwata, S.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	X-ray Free-Electron Laser Priority Strategy Program

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-22
  Changes: Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary