5K2C

1.9 angstrom A2a adenosine receptor structure with sulfur SAD phasing and phase extension using XFEL data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

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

  • DOI: 10.1126/sciadv.1600292
  • Primary Citation of Related Structures:  

  • 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 a ...

    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.


    Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.,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.; 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.,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.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Physics, Arizona State University, 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.,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 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosine receptor A2a/Soluble cytochrome b562 chimera
A
447Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybC, ADORA2A (ADORA2)
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Go to Gene View: ADORA2A
Go to UniProtKB:  P29274
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

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A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
ZMA
Query on ZMA

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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
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CLR
Query on CLR

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A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZMAKd: 0.2 nM (88) BINDINGDB
ZMAKi: 0.1 - 64 nM (88) BINDINGDB
ZMAIC50: 0.7 - 33 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 40.360α = 90.00
b = 180.740β = 90.00
c = 142.800γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
SHELXDphasing
CrystFELdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references
  • Version 1.2: 2016-11-23
    Type: Structure summary
  • Version 1.3: 2017-11-22
    Type: Refinement description
  • Version 1.4: 2018-02-14
    Type: Data collection
  • Version 1.5: 2018-11-28
    Type: Data collection