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- EMDB-73782: The structure of short splice variant (Q9UBL9-2) of human P2X2 re... -

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Basic information

Entry
Database: EMDB / ID: EMD-73782
TitleThe structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with Mg-ATP
Map dataCryoSPARC sharpened map
Sample
  • Complex: The structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with Mg-ATP
    • Protein or peptide: Isoform B of P2X purinoceptor 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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 / neuromuscular junction development ...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 / neuromuscular junction development / response to ATP / 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: 2.83 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: To Be Published
Title: The structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with Mg-ATP
Authors: Dhingra S / Swartz KJ
History
DepositionNov 5, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73782.png

Downloads & links

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Map

FileDownload / File: emd_73782.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 247.2 Å		0.82 Å/pix.
x 300 pix.
= 247.2 Å		0.82 Å/pix.
x 300 pix.
= 247.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.1711408 - 0.33283648
Average (Standard dev.)0.00033109414 (±0.007526692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_73782_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map

Fileemd_73782_additional_2.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73782_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73782_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: The structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with Mg-ATP
Components
  • Complex: The structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with Mg-ATP
    • Protein or peptide: Isoform B of P2X purinoceptor 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: The structure of short splice variant (Q9UBL9-2) of human P2X2 re...

SupramoleculeName: The structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with Mg-ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform B of P2X purinoceptor 2

MacromoleculeName: Isoform B of P2X purinoceptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.896434 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 KFDKMVDTPA SEPAQASTPT DPKG LAQL

UniProtKB: P2X purinoceptor 2

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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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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 (Q9UBL9-2) in lipid nanodiscs with Mg-ATP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 59.34 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: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 344336
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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