[English] 日本語
Yorodumi
- EMDB-70526: Human P2X2 receptor channel in detergent with residual ATP after ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70526
TitleHuman P2X2 receptor channel in detergent with residual ATP after apyrase treatment
Map data
Sample
  • Complex: Human P2X2 receptor channel in detergent with residual ATP after apyrase treatment
    • Protein or peptide: Human P2X purinoceptor 2
KeywordsATP-gated ion channel / MEMBRANE PROTEIN
Function / homologyIsoform A of P2X purinoceptor 2
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 6, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70526.png

Downloads & links

-
Map

FileDownload / File: emd_70526.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0428
Minimum - Maximum-0.091007456 - 0.24520618
Average (Standard dev.)0.00076973444 (±0.0056835124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_70526_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_70526_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70526_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_70526_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human P2X2 receptor channel in detergent with residual ATP after ...

EntireName: Human P2X2 receptor channel in detergent with residual ATP after apyrase treatment
Components
  • Complex: Human P2X2 receptor channel in detergent with residual ATP after apyrase treatment
    • Protein or peptide: Human P2X purinoceptor 2

-
Supramolecule #1: Human P2X2 receptor channel in detergent with residual ATP after ...

SupramoleculeName: Human P2X2 receptor channel in detergent with residual ATP after apyrase treatment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Human P2X purinoceptor 2

MacromoleculeName: Human P2X purinoceptor 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
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 VCTPSHPSGS WPVTLARVLG QAPPEPGHRS EDQHPSPPSG QEGQQGAECG PAFPPLRPCP ISAPSEQMVD TPASEPAQAS TPTDPKGLAQ L

UniProtKB: Isoform A of P2X purinoceptor 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 56.8 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

+
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162474
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more