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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: To Be Published
Title: The structure of human P2X2 receptor channel in lipid nanodiscs
Authors: Dhingra S / Swartz KJ
History
DepositionApr 30, 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_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

Size
Brightness
Contrast
Others
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

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: 0.0424
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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AxesZYX

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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
Projections & Slices
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Density Histograms

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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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