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- EMDB-70602: The pre-desensitized state structure of human P2X2 receptor chann... -

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Basic information

Entry
Database: EMDB / ID: EMD-70602
TitleThe pre-desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium
Map data
Sample
  • Complex: The pre-desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium
    • Protein or peptide: P2X purinoceptor 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsATP-gated ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


detection of hypoxic conditions in blood by carotid body chemoreceptor signaling / Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / peristalsis / Elevation of cytosolic Ca2+ levels / neuromuscular synaptic transmission / urinary bladder smooth muscle contraction / response to carbohydrate / response to ATP ...detection of hypoxic conditions in blood by carotid body chemoreceptor signaling / Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / peristalsis / Elevation of cytosolic Ca2+ levels / neuromuscular synaptic transmission / urinary bladder smooth muscle contraction / response to carbohydrate / response to ATP / neuromuscular junction development / behavioral response to pain / positive regulation of calcium ion transport into cytosol / ligand-gated monoatomic ion channel activity / neuronal dense core vesicle / skeletal muscle fiber development / positive regulation of calcium-mediated signaling / response to ischemia / sensory perception of sound / calcium ion transmembrane transport / sensory perception of taste / response to hypoxia / signaling receptor complex / apical plasma membrane / postsynapse / neuronal cell body / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
P2X2 purinoceptor / : / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 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
DepositionMay 13, 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_70602.png

Downloads & links

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Map

FileDownload / File: emd_70602.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0017392508 - 1.4899473
Average (Standard dev.)0.0005926542 (±0.017202122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70602_additional_1.map
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Half map: #2

Fileemd_70602_half_map_1.map
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Half map: #1

Fileemd_70602_half_map_2.map
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Sample components

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Entire : The pre-desensitized state structure of human P2X2 receptor chann...

EntireName: The pre-desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium
Components
  • Complex: The pre-desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium
    • Protein or peptide: P2X purinoceptor 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The pre-desensitized state structure of human P2X2 receptor chann...

SupramoleculeName: The pre-desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.814996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAQPKYPA GATARRLARG CWSALWDYET PKVIVVRNRR LGVLYRAVQL LILLYFVWYV FIVQKSYQES ETGPESSIIT KVKGITTSE HKVWDVEEYV KPPEGGSVFS IITRVEATHS QTQGTCPESI RVHNATCLSD ADCVAGELDM LGNGLRTGRC V PYYQGPSK ...String:
MAAAQPKYPA GATARRLARG CWSALWDYET PKVIVVRNRR LGVLYRAVQL LILLYFVWYV FIVQKSYQES ETGPESSIIT KVKGITTSE HKVWDVEEYV KPPEGGSVFS IITRVEATHS QTQGTCPESI RVHNATCLSD ADCVAGELDM LGNGLRTGRC V PYYQGPSK TCEVFGWCPV EDGASVSQFL GTMAPNFTIL IKNSIHYPKF HFSKGNIADR TDGYLKRCTF HEASDLYCPI FK LGFIVEK AGESFTELAH KGGVIGVIIN WDCDLDLPAS ECNPKYSFRR LDPKHVPASS GYNFRFAKYY KINGTTTRTL IKA YGIRID VIVHGQAGKF SLIPTIINLA TALTSVGVGS FLCDWILLTF MNKNKVYSHK KFDKVCTPSH PSGSWPVTLA RVLG QAPPE PGHRSEDQHP SPPSGQEGQQ GAECGPAFPP LRPCPISAPS EQMVDTPASE PAQASTPTDP KGLAQL

UniProtKB: P2X purinoceptor 2

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
VitrificationCryogen name: ETHANE
DetailsHuman P2X2 receptor channel in lipid nanodiscs with free ATP and sodium

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 59.9 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: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 243758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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