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- EMDB-41582: Cryo-EM structure of the rat P2X7 receptor in complex with the al... -

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Basic information

Entry
Database: EMDB / ID: EMD-41582
TitleCryo-EM structure of the rat P2X7 receptor in complex with the allosteric antagonist methyl blue
Map dataSharpened volume for methyl blue bound to rP2X7
Sample
  • Complex: Membrane protein
    • Protein or peptide: P2X purinoceptor 7
  • Ligand: 4,4',4''-[methanetriyltris(4,1-phenyleneazanediyl)]tri(benzene-1-sulfonic acid)
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID
  • Ligand: water
KeywordsMembrane Protein / Ion Channel / Ligand-gate Ion Channel / P2X Receptor / Allosteric Antagonist / High-Affinity Agonist
Function / homology
Function and homology information


Platelet homeostasis / The NLRP3 inflammasome / positive regulation of lymphocyte apoptotic process / regulation of presynaptic dense core granule exocytosis / positive regulation of bleb assembly / NAD transport / Elevation of cytosolic Ca2+ levels / phagolysosome assembly / phospholipid transfer to membrane / positive regulation of cytoskeleton organization ...Platelet homeostasis / The NLRP3 inflammasome / positive regulation of lymphocyte apoptotic process / regulation of presynaptic dense core granule exocytosis / positive regulation of bleb assembly / NAD transport / Elevation of cytosolic Ca2+ levels / phagolysosome assembly / phospholipid transfer to membrane / positive regulation of cytoskeleton organization / positive regulation of monoatomic ion transmembrane transport / purinergic nucleotide receptor signaling pathway / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / collagen metabolic process / positive regulation of interleukin-1 alpha production / ATP export / pore complex assembly / negative regulation of cell volume / positive regulation of prostaglandin secretion / plasma membrane phospholipid scrambling / bleb assembly / vesicle budding from membrane / positive regulation of T cell apoptotic process / bleb / response to fluid shear stress / programmed cell death / positive regulation of ossification / cellular response to dsRNA / cell volume homeostasis / ceramide biosynthetic process / negative regulation of bone resorption / positive regulation of glutamate secretion / skeletal system morphogenesis / positive regulation of macrophage cytokine production / phospholipid translocation / response to zinc ion / sodium channel activity / protein homotrimerization / response to ATP / positive regulation of mitochondrial depolarization / positive regulation of NLRP3 inflammasome complex assembly / T cell homeostasis / membrane protein ectodomain proteolysis / response to electrical stimulus / positive regulation of calcium ion transport into cytosol / synaptic vesicle exocytosis / membrane depolarization / monoatomic cation transport / T cell proliferation / positive regulation of bone mineralization / potassium channel activity / response to mechanical stimulus / neuronal action potential / regulation of sodium ion transport / extrinsic apoptotic signaling pathway / negative regulation of MAPK cascade / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / sensory perception of pain / reactive oxygen species metabolic process / establishment of localization in cell / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / positive regulation of protein secretion / protein serine/threonine kinase activator activity / protein catabolic process / response to bacterium / neuromuscular junction / apoptotic signaling pathway / mitochondrion organization / lipopolysaccharide binding / protein processing / response to calcium ion / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / calcium ion transmembrane transport / cell morphogenesis / terminal bouton / cell-cell junction / calcium ion transport / nuclear envelope / signaling receptor activity / channel activity / scaffold protein binding / response to lipopolysaccharide / gene expression / positive regulation of MAPK cascade / cell surface receptor signaling pathway / postsynapse / defense response to Gram-positive bacterium / positive regulation of apoptotic process / response to xenobiotic stimulus / inflammatory response / copper ion binding / signaling receptor binding / external side of plasma membrane / neuronal cell body
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 speciesRattus (rats)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsOken AC / Ditter IA / Lisi NE / Krishnamurthy I / McCarthy AE / Godsey MH / Mansoor SE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R00HL138129 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM149551 United States
CitationJournal: Sci Adv / Year: 2024
Title: P2X receptors exhibit at least three modes of allosteric antagonism.
Authors: Adam C Oken / Ismayn A Ditter / Nicolas E Lisi / Ipsita Krishnamurthy / Michael H Godsey / Steven E Mansoor /
Abstract: P2X receptors are trimeric ion channels activated by adenosine triphosphate (ATP) that contribute to pathophysiological processes ranging from asthma to neuropathic pain and neurodegeneration. A ...P2X receptors are trimeric ion channels activated by adenosine triphosphate (ATP) that contribute to pathophysiological processes ranging from asthma to neuropathic pain and neurodegeneration. A number of small-molecule antagonists have been identified for these important pharmaceutical targets. However, the molecular pharmacology of P2X receptors is poorly understood because of the chemically disparate nature of antagonists and their differential actions on the seven constituent subtypes. Here, we report high-resolution cryo-electron microscopy structures of the homomeric rat P2X receptor bound to five previously known small-molecule allosteric antagonists and a sixth antagonist that we identify. Our structural, biophysical, and electrophysiological data define the molecular determinants of allosteric antagonism in this pharmacologically relevant receptor, revealing three distinct classes of antagonists that we call shallow, deep, and starfish. Starfish binders, exemplified by the previously unidentified antagonist methyl blue, represent a unique class of inhibitors with distinct functional properties that could be exploited to develop potent P2X ligands with substantial clinical impact.
History
DepositionAug 9, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41582.png

Downloads & links

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Map

FileDownload / File: emd_41582.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened volume for methyl blue bound to rP2X7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 600 pix.
= 388.8 Å		0.65 Å/pix.
x 600 pix.
= 388.8 Å		0.65 Å/pix.
x 600 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.1596221 - 1.4592301
Average (Standard dev.)0.00017485864 (±0.018530896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 388.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41582_msk_1.map
Projections & Slices
AxesZYX

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Additional map: locally sharpened local refinement volume for methyl blue...

Fileemd_41582_additional_1.map
Annotationlocally sharpened local refinement volume for methyl blue bound to rP2X7
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Unsharpened volume for methyl blue bound to rP2X7

Fileemd_41582_additional_2.map
AnnotationUnsharpened volume for methyl blue bound to rP2X7
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map A for methyl blue bound to rP2X7

Fileemd_41582_half_map_1.map
AnnotationHalf map A for methyl blue bound to rP2X7
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map B for methyl blue bound to rP2X7

Fileemd_41582_half_map_2.map
AnnotationHalf map B for methyl blue bound to rP2X7
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane protein

EntireName: Membrane protein
Components
  • Complex: Membrane protein
    • Protein or peptide: P2X purinoceptor 7
  • Ligand: 4,4',4''-[methanetriyltris(4,1-phenyleneazanediyl)]tri(benzene-1-sulfonic acid)
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: Membrane protein

SupramoleculeName: Membrane protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus (rats)

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Macromolecule #1: P2X purinoceptor 7

MacromoleculeName: P2X purinoceptor 7 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus (rats)
Molecular weightTheoretical: 68.472461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPACCSWNDV FQYETNKVTR IQSVNYGTIK WILHMTVFSY VSFALMSDKL YQRKEPLISS VHTKVKGVAE VTENVTEGGV TKLVHGIFD TADYTLPLQG NSFFVMTNYL KSEGQEQKLC PEYPSRGKQC HSDQGCIKGW MDPQSKGIQT GRCIPYDQKR K TCEIFAWC ...String:
MPACCSWNDV FQYETNKVTR IQSVNYGTIK WILHMTVFSY VSFALMSDKL YQRKEPLISS VHTKVKGVAE VTENVTEGGV TKLVHGIFD TADYTLPLQG NSFFVMTNYL KSEGQEQKLC PEYPSRGKQC HSDQGCIKGW MDPQSKGIQT GRCIPYDQKR K TCEIFAWC PAEEGKEAPR PALLRSAENF TVLIKNNIDF PGHNYTTRNI LPGMNISCTF HKTWNPQCPI FRLGDIFQEI GE NFTEVAV QGGIMGIEIY WDCNLDSWSH RCQPKYSFRR LDDKYTNESL FPGYNFRYAK YYKENGMEKR TLIKAFGVRF DIL VFGTGG KFDIIQLVVY IGSTLSYFGL ATVCIDLIIN TYASTCCRSR VYPSCKCCEP CAVNEYYYRK KCEPIVEPKP TLKY VSFVD EPHIWMVDQQ LLGKSLQDVK GQEVPRPQTD FLELSRLSLS LHHSPPIPGQ PEEMQLLQIE AVPRSRDSPD WCQCG NCLP SQLPENRRAL EELCCRRKPG QCITTSELFS KIVLSREALQ LLLLYQEPLL ALEGEAINSK LRHCAYRSYA TWRFVS QDM ADFAILPSCC RWKIRKEFPK TQGQYSGFKY PY

UniProtKB: P2X purinoceptor 7

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Macromolecule #2: 4,4',4''-[methanetriyltris(4,1-phenyleneazanediyl)]tri(benzene-1-...

MacromoleculeName: 4,4',4''-[methanetriyltris(4,1-phenyleneazanediyl)]tri(benzene-1-sulfonic acid)
type: ligand / ID: 2 / Number of copies: 3 / Formula: KFM
Molecular weightTheoretical: 757.852 Da

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 15 / Formula: PLM
Source (natural)Organism: Rattus (rats)
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 85 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 9902 / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: PDB ENTRY
PDB model - PDB ID:

6u9v

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 341185
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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