5K2D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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:  
    5K2D, 5K2A, 5K2C, 5K2B

  • 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 ...

    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 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosine receptor A2a/Soluble cytochrome b562 chimeraA447Homo sapiensEscherichia coli
This entity is chimeric
Mutation(s): 3 
Gene Names: ADORA2AADORA2
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
OLB (Subject of Investigation/LOI)
Query on OLB

Download Ideal Coordinates CCD File 
G [auth A], K [auth A](2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
ZMA (Subject of Investigation/LOI)
Query on ZMA

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
OLA (Subject of Investigation/LOI)
Query on OLA

Download Ideal Coordinates CCD File 
AA [auth A] , BA [auth A] , N [auth A] , O [auth A] , P [auth A] , Q [auth A] , R [auth A] , S [auth A] , 
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
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
Z [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZMA BindingDB:  5K2D 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: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.36α = 90
b = 180.74β = 90
c = 142.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • 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