5K2D | pdb_00005k2d

1.9A angstrom A2a adenosine receptor structure with MR phasing using XFEL data

• PDB DOI: https://doi.org/10.2210/pdb5K2D/pdb

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


• Deposited: 2016-05-18 Released: 2016-09-21 
• Deposition Author(s): Batyuk, A., Galli, L., Ishchenko, A., Han, G.W., Gati, C., Popov, P., Lee, M.-Y., Stauch, B., White, T.A., Barty, A., Aquila, A., Hunter, M.S., Liang, M., Boutet, S., Pu, M., Liu, Z.-J., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J.C.H., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Native phasing of x-ray free-electron laser data for a G protein-coupled receptor.

Batyuk, A., Galli, L., Ishchenko, A., Han, G.W., Gati, C., Popov, P.A., Lee, M.Y., Stauch, B., White, T.A., Barty, A., Aquila, A., Hunter, M.S., Liang, M., Boutet, S., Pu, M., Liu, Z.J., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J.C., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R.C., Cherezov, V.

(2016) Sci Adv 2: e1600292-e1600292

• PubMed: 27679816 
• DOI: https://doi.org/10.1126/sciadv.1600292
• Primary Citation Related Structures: 
  5K2A, 5K2B, 5K2C, 5K2D


• PubMed Abstract: 
  

  Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of "diffraction-before-destruction." However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A _2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.; iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
Center for Applied Structural Discovery at the Biodesign Institute, School of Molecular Sciences, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA.
Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.27 kDa 
• Atom Count: 3,636 
• Modeled Residue Count: 395 
• 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 chimera	A	447	Homo sapiens, Escherichia coli This entity is chimeric	Mutation(s): 3  Gene Names: ADORA2A, ADORA2 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	D [auth A], E [auth A], F [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC	H [auth A], I [auth A], J [auth A], L [auth A], M [auth A], U [auth A], V [auth A], W [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLB	G [auth A], K [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-QJRAZLAKSA-N
ZMA	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	AA [auth A], BA [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], X [auth A], Y [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG	Z [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.36	α = 90
b = 180.74	β = 90
c = 142.8	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Batyuk, A., Galli, L., Ishchenko, A., Han, G.W., Gati, C., Popov, P., Lee, M.-Y., Stauch, B., White, T.A., Barty, A., Aquila, A., Hunter, M.S., Liang, M., Boutet, S., Pu, M., Liu, Z.-J., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J.C.H., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-10-12
  Changes: Database references
• Version 1.2: 2016-11-23
  Changes: Structure summary
• Version 1.3: 2018-02-14
  Changes: Data collection
• Version 1.4: 2018-11-28
  Changes: Data collection
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2024-10-23
  Changes: Structure summary