9FUP

Serial microseconds crystallography at ID29 using fixed-target (small foils): A2a adenosine receptor co-crystallised with Istradefylline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.

Orlans, J.Rose, S.L.Ferguson, G.Oscarsson, M.Homs Puron, A.Beteva, A.Debionne, S.Theveneau, P.Coquelle, N.Kieffer, J.Busca, P.Sinoir, J.Armijo, V.Lopez Marrero, M.Felisaz, F.Papp, G.Gonzalez, H.Caserotto, H.Dobias, F.Gigmes, J.Lebon, G.Basu, S.de Sanctis, D.

(2025) Commun Chem 8: 6-6

  • DOI: https://doi.org/10.1038/s42004-024-01404-y
  • Primary Citation of Related Structures:  
    9FTS, 9FTU, 9FTV, 9FTX, 9FTY, 9FU1, 9FUD, 9FUE, 9FUP

  • PubMed Abstract: 

    Serial macromolecular crystallography has become a powerful method to reveal room temperature structures of biological macromolecules and perform time-resolved studies. ID29, a flagship beamline of the ESRF 4th generation synchrotron, is the first synchrotron beamline in the world capable of delivering high brilliance microsecond X-ray pulses at high repetition rate for the structure determination of biological macromolecules at room temperature. The cardinal combination of microsecond exposure times, innovative beam characteristics and adaptable sample environment provides high quality complete data, even from an exceptionally small amount of crystalline material, enabling what we collectively term serial microsecond crystallography (SµX). After validating the use of different sample delivery methods with various model systems, we applied SµX to an integral membrane receptor, where only a few thousands diffraction images were sufficient to obtain a fully interpretable electron density map for the antagonist istradefylline-bound A 2A receptor conformation, providing access to the antagonist binding mode. SµX, as demonstrated at ID29, will quickly find its broad applicability at upcoming 4th generation synchrotron sources worldwide and opens a new frontier in time-resolved SµX.


  • Organizational Affiliation

    ESRF - The European Synchrotron, 71 Avenue des Martyrs, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine receptor A2a,Soluble cytochrome b562423Homo sapiensMutation(s): 0 
Gene Names: ADORA2AADORA2cybC
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P29274
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
JQ9 (Subject of Investigation/LOI)
Query on JQ9

Download Ideal Coordinates CCD File 
U [auth A]8-[(~{E})-2-(3,4-dimethoxyphenyl)ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione
C20 H24 N4 O4
IQVRBWUUXZMOPW-PKNBQFBNSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
S [auth A],
T [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLB
Query on OLB

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A]
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [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]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.17α = 90
b = 179.4β = 90
c = 142.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-20-CE11-0019

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release