9FUP | pdb_00009fup

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

PDB DOI: https://doi.org/10.2210/pdb9FUP/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2024-06-26 Released: 2025-01-22
Deposition Author(s): Orlans, J., Rose, S.L., Ferguson, G., Lebon, G., Basu, S., de Sanctis, D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.288 (Depositor), 0.288 (DCC)
R-Value Work:
0.251 (Depositor), 0.251 (DCC)
R-Value Observed:
0.255 (Depositor)

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

PubMed: 39775172 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42004-024-01404-y
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 52.72 kDa
Atom Count: 3,205
Modeled Residue Count: 383
Deposited Residue Count: 423
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a,Soluble cytochrome b562	A	423	Homo sapiens	Mutation(s): 0 Gene Names: ADORA2A, ADORA2, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P29274 (Homo sapiens) Explore P29274 Go to UniProtKB: P29274
PHAROS: P29274 GTEx: ENSG00000128271
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
JQ9 (Subject of Investigation/LOI) Query on JQ9 Download:Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	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		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	S [auth A], T [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain S [auth A] Focus chain T [auth A]
OLB Query on OLB Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	Q [auth A], R [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A]
OLA Query on OLA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]