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- EMDB-39716: Cryo-EM structures of the panda P2X7 receptor in complex with JNJ... -

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Basic information

Entry
Database: EMDB / ID: EMD-39716
TitleCryo-EM structures of the panda P2X7 receptor in complex with JNJ-54175446
Map data
Sample
  • Complex: P2X7 trimer
    • Protein or peptide: P2X purinoceptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: [2-chloranyl-3-(trifluoromethyl)phenyl]-[(4~{R})-1-(5-fluoranylpyrimidin-2-yl)-4-methyl-6,7-dihydro-4~{H}-[1,2,3]triazolo[4,5-c]pyridin-5-yl]methanone
KeywordsChannel / TRANSPORT PROTEIN
Function / homology
Function and homology information


extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / response to ATP / calcium ion transmembrane transport / postsynapse / ATP binding / plasma membrane
Similarity search - Function
P2X purinoreceptor 7, intracellular domain / P2X purinoreceptor 7 intracellular domain / P2X7 purinoceptor / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
Biological speciesAiluropoda melanoleuca (giant panda)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSheng D / Hattori M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of the panda P2X7 receptor in complex with JNJ-54175446
Authors: Sheng D / Hattori M
History
DepositionApr 10, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39716.png

Downloads & links

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Map

FileDownload / File: emd_39716.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.438
Minimum - Maximum-2.82735 - 3.934174
Average (Standard dev.)0.0015271065 (±0.10551961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39716_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_39716_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 : P2X7 trimer

EntireName: P2X7 trimer
Components
  • Complex: P2X7 trimer
    • Protein or peptide: P2X purinoceptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: [2-chloranyl-3-(trifluoromethyl)phenyl]-[(4~{R})-1-(5-fluoranylpyrimidin-2-yl)-4-methyl-6,7-dihydro-4~{H}-[1,2,3]triazolo[4,5-c]pyridin-5-yl]methanone

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Supramolecule #1: P2X7 trimer

SupramoleculeName: P2X7 trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ailuropoda melanoleuca (giant panda)

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Macromolecule #1: P2X purinoceptor

MacromoleculeName: P2X purinoceptor / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ailuropoda melanoleuca (giant panda)
Molecular weightTheoretical: 38.716234 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSSTNYGTIK WIFHALVFSY ISFALISDKR YQKKEPLISS VHTKVKGIAE VKAEILENGM KKMVSGVFDT ADYTFPLQGN SFFVMTNFI KTEGQQQGLC PDFPTARTIC SSDRGCKKGR MDPQSKGIQT GRCVVYKERL KTCEVSAWCP IEEVKDAPRP A LLNSAENF ...String:
GSSTNYGTIK WIFHALVFSY ISFALISDKR YQKKEPLISS VHTKVKGIAE VKAEILENGM KKMVSGVFDT ADYTFPLQGN SFFVMTNFI KTEGQQQGLC PDFPTARTIC SSDRGCKKGR MDPQSKGIQT GRCVVYKERL KTCEVSAWCP IEEVKDAPRP A LLNSAENF TVLIKNNIDF PGHNYTTRNI LPGVNITCTF HKTQNPQCPI FRLGDIFQET GDSFSDVAIQ GGIMGIEIYW DC NLDGWFH HCRPKYSFRR LDDKTTSESL YPGYNFRYAK YYKENNVEKR TLIKVFGIRF DILVFGTGGK FNVIQLAVYI GSV ISYFGL ATVFIDILIN TYSASS

UniProtKB: P2X purinoceptor

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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: [2-chloranyl-3-(trifluoromethyl)phenyl]-[(4~{R})-1-(5-fluoranylpy...

MacromoleculeName: [2-chloranyl-3-(trifluoromethyl)phenyl]-[(4~{R})-1-(5-fluoranylpyrimidin-2-yl)-4-methyl-6,7-dihydro-4~{H}-[1,2,3]triazolo[4,5-c]pyridin-5-yl]methanone
type: ligand / ID: 3 / Number of copies: 3 / Formula: A1L0I
Molecular weightTheoretical: 440.782 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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 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: OTHER / Details: CryoSPARC ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135394
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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