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- EMDB-70456: The structure of short splice variant (Q9UBL9-2) of human P2X2 re... -

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Basic information

Entry
Database: EMDB / ID: EMD-70456
TitleThe structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with 5mM MgCl2
Map data
Sample
  • Complex: Short splice variant (Q9UBL9-2) of human P2X2 in lipid nanodiscs with 5mM MgCl2
    • Protein or peptide: P2X purinoceptor 2
KeywordsATP-gated ion channel / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsDhingra S / Swartz KJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS003018 United States
CitationJournal: Sci Adv / Year: 2026
Title: Mechanisms of ligand recognition and channel opening for P2X2 receptors in lipid nanodiscs.
Authors: Surbhi Dhingra / Maia Moog / Kenton J Swartz /
Abstract: Extracellular adenosine 5'-triphosphate (ATP) activates P2X receptor channels (P2XRs) that serve important roles in the immune and nervous systems. Available structures of P2XRs in detergents reveal ...Extracellular adenosine 5'-triphosphate (ATP) activates P2X receptor channels (P2XRs) that serve important roles in the immune and nervous systems. Available structures of P2XRs in detergents reveal that ATP binding to the extracellular domain leads to severing of subunit interfaces within transmembrane regions as the pore opens. Here we report cryo-electron microscopy structures of the human P2X2R in lipid nanodiscs in an apo closed state, with ATP, Mg-ATP, and suramin bound. We find that a unique Arg residue interacts with the γ-PO of ATP in P2X2R and underlies the requirement of this subtype for ATP. Channel opening and desensitization occur when ATP binds, whereas the channel remains closed when Mg-ATP binds. A continuous belt of partially resolved lipids in the outer leaflet stabilizes the closed state, and the presence of lipids prevents the severing of subunit interfaces as the channel opens. These findings establish key mechanistic principles of gating for P2X2R in a membrane-like environment, providing a framework for future mechanistic studies and therapeutic development.
History
DepositionApr 30, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70456.png

Downloads & links

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Map

FileDownload / File: emd_70456.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 270 pix.
= 222.48 Å		0.82 Å/pix.
x 270 pix.
= 222.48 Å		0.82 Å/pix.
x 270 pix.
= 222.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0424
Minimum - Maximum-0.18843071 - 0.35255876
Average (Standard dev.)0.0010774799 (±0.00926518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 222.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70456_msk_1.map
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Additional map: #1

Fileemd_70456_additional_1.map
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Half map: #2

Fileemd_70456_half_map_1.map
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Half map: #1

Fileemd_70456_half_map_2.map
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Sample components

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Entire : Short splice variant (Q9UBL9-2) of human P2X2 in lipid nanodiscs ...

EntireName: Short splice variant (Q9UBL9-2) of human P2X2 in lipid nanodiscs with 5mM MgCl2
Components
  • Complex: Short splice variant (Q9UBL9-2) of human P2X2 in lipid nanodiscs with 5mM MgCl2
    • Protein or peptide: P2X purinoceptor 2

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Supramolecule #1: Short splice variant (Q9UBL9-2) of human P2X2 in lipid nanodiscs ...

SupramoleculeName: Short splice variant (Q9UBL9-2) of human P2X2 in lipid nanodiscs with 5mM MgCl2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: P2X purinoceptor 2

MacromoleculeName: P2X purinoceptor 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MAAAQPKYPA GATARRLARG CWSALWDYET PKVIVVRNRR LGVLYRAVQL LILLYFVWYV FIVQKSYQES ETGPESSIIT KVKGITTSEH KVWDVEEYVK PPEGGSVFSI ITRVEATHSQ TQGTCPESIR VHNATCLSDA DCVAGELDML GNGLRTGRCV PYYQGPSKTC ...String:
MAAAQPKYPA GATARRLARG CWSALWDYET PKVIVVRNRR LGVLYRAVQL LILLYFVWYV FIVQKSYQES ETGPESSIIT KVKGITTSEH KVWDVEEYVK PPEGGSVFSI ITRVEATHSQ TQGTCPESIR VHNATCLSDA DCVAGELDML GNGLRTGRCV PYYQGPSKTC EVFGWCPVED GASVSQFLGT MAPNFTILIK NSIHYPKFHF SKGNIADRTD GYLKRCTFHE ASDLYCPIFK LGFIVEKAGE SFTELAHKGG VIGVIINWDC DLDLPASECN PKYSFRRLDP KHVPASSGYN FRFAKYYKIN GTTTRTLIKA YGIRIDVIVH GQAGKFSLIP TIINLATALT SVGVGSFLCD WILLTFMNKN KVYSHKKFDK MVDTPASEPA QASTPTDPKG LAQL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.73 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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