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- EMDB-64566: Cryo-EM structure of the human P2X2 receptor in the apo closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-64566
TitleCryo-EM structure of the human P2X2 receptor in the apo closed state
Map data
Sample
  • Complex: P2X purinoceptor 2
    • Protein or peptide: P2X purinoceptor 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)
  • Ligand: SODIUM ION
KeywordsP2X ion channal / 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: 2.19 Å
AuthorsZhang J / Cheng XY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the human P2X2 receptor in the apo closed state
Authors: Zhang J / Cheng XY
History
DepositionMay 13, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64566.png

Downloads & links

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Map

FileDownload / File: emd_64566.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.)
0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.51019967 - 1.472399
Average (Standard dev.)-0.001226795 (±0.026972864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64566_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64566_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 : P2X purinoceptor 2

EntireName: P2X purinoceptor 2
Components
  • Complex: P2X purinoceptor 2
    • Protein or peptide: P2X purinoceptor 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)
  • Ligand: SODIUM ION

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Supramolecule #1: P2X purinoceptor 2

SupramoleculeName: P2X purinoceptor 2 / 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: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / 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: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)

MacromoleculeName: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL) / type: ligand / ID: 3 / Number of copies: 3 / Formula: PG8
Molecular weightTheoretical: 497.537 Da
Chemical component information

ChemComp-PG8:
1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 285888
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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