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- EMDB-20702: EMDB: Cryo electron microscopy map of the ATP-gated rat P2X7 ion ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20702
TitleEMDB: Cryo electron microscopy map of the ATP-gated rat P2X7 ion channel in the apo, closed state
Map dataOverall map for the apo- (closed) state of rat P2X7 receptor
Sample
  • Complex: P2X7 receptor ion channel
    • Protein or peptide: P2X purinoceptor 7
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine
  • Ligand: PALMITIC ACID
Function / homology
Function and homology information


Platelet homeostasis / The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly / NAD transport / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / phospholipid transfer to membrane / positive regulation of cytoskeleton organization ...Platelet homeostasis / The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly / NAD transport / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / phospholipid transfer to membrane / positive regulation of cytoskeleton organization / purinergic nucleotide receptor signaling pathway / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / lymphocyte apoptotic process / positive regulation of monoatomic ion transmembrane transport / gamma-aminobutyric acid secretion / pore complex assembly / positive regulation of interleukin-1 alpha production / plasma membrane organization / negative regulation of cell volume / positive regulation of gamma-aminobutyric acid secretion / ATP export / bleb / collagen metabolic process / plasma membrane phospholipid scrambling / response to fluid shear stress / T cell apoptotic process / positive regulation of prostaglandin secretion / bleb assembly / positive regulation of T cell apoptotic process / mitochondrial depolarization / vesicle budding from membrane / prostaglandin secretion / ceramide biosynthetic process / cellular response to dsRNA / programmed cell death / positive regulation of glutamate secretion / positive regulation of ossification / cell volume homeostasis / glutamate secretion / skeletal system morphogenesis / negative regulation of bone resorption / phospholipid translocation / positive regulation of macrophage cytokine production / positive regulation of calcium ion transport into cytosol / response to ATP / positive regulation of mitochondrial depolarization / response to zinc ion / T cell homeostasis / cellular response to organic cyclic compound / monoatomic cation transport / synaptic vesicle exocytosis / membrane depolarization / membrane protein ectodomain proteolysis / neuronal action potential / protein secretion / negative regulation of MAPK cascade / response to electrical stimulus / positive regulation of bone mineralization / response to mechanical stimulus / T cell proliferation / regulation of sodium ion transport / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / sensory perception of pain / positive regulation of glycolytic process / reactive oxygen species metabolic process / protein serine/threonine kinase activator activity / positive regulation of interleukin-1 beta production / mitochondrion organization / establishment of localization in cell / positive regulation of protein secretion / apoptotic signaling pathway / calcium ion transmembrane transport / lipopolysaccharide binding / response to bacterium / neuromuscular junction / cell morphogenesis / protein catabolic process / response to organic cyclic compound / terminal bouton / T cell mediated cytotoxicity / protein processing / positive regulation of interleukin-6 production / response to calcium ion / channel activity / positive regulation of T cell mediated cytotoxicity / calcium ion transport / MAPK cascade / cell-cell junction / nuclear envelope / signaling receptor activity / gene expression / scaffold protein binding / postsynapse / response to lipopolysaccharide / positive regulation of MAPK cascade / cell surface receptor signaling pathway / defense response to Gram-positive bacterium
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 norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMansoor SE / McCarthy AE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K99HL138129 United States
CitationJournal: Cell / Year: 2019
Title: Full-Length P2X Structures Reveal How Palmitoylation Prevents Channel Desensitization.
Authors: Alanna E McCarthy / Craig Yoshioka / Steven E Mansoor /
Abstract: P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and ...P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and tumor progression pathways. It is the most structurally and functionally distinct P2X subtype, containing a unique cytoplasmic domain critical for the receptor to initiate apoptosis and not undergo desensitization. However, lack of structural information about the cytoplasmic domain has hindered understanding of the molecular mechanisms underlying these processes. We report cryoelectron microscopy structures of full-length rat P2X receptor in apo and ATP-bound states. These structures reveal how one cytoplasmic element, the C-cys anchor, prevents desensitization by anchoring the pore-lining helix to the membrane with palmitoyl groups. They show a second cytoplasmic element with a unique fold, the cytoplasmic ballast, which unexpectedly contains a zinc ion complex and a guanosine nucleotide binding site. Our structures provide first insights into the architecture and function of a P2X receptor cytoplasmic domain.
History
DepositionSep 9, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseOct 23, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0349
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0349
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6u9v
  • Surface level: 0.0349
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20702.png

Downloads & links

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Map

FileDownload / File: emd_20702.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map for the apo- (closed) state of rat P2X7 receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0349 / Movie #1: 0.0349
Minimum - Maximum-0.15550219 - 0.2761771
Average (Standard dev.)0.0000428620 (±0.0065663885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z334.400334.400334.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1560.2760.000

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Supplemental data

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Additional map: Map for the apo- (closed) state of rat...

Fileemd_20702_additional_1.map
AnnotationMap for the apo- (closed) state of rat P2X7 receptor from a focused refinement using a mask that includes the transmembrane domain and the cytoplasmic domain but excludes the extracellular domain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map for the apo- (closed) state of rat...

Fileemd_20702_additional_2.map
AnnotationMap for the apo- (closed) state of rat P2X7 receptor from a focused refinement using a mask that includes the extracellular domain but excludes the transmembrane domain and the cytoplasmic domain
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 receptor ion channel

EntireName: P2X7 receptor ion channel
Components
  • Complex: P2X7 receptor ion channel
    • Protein or peptide: P2X purinoceptor 7
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine
  • Ligand: PALMITIC ACID

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Supramolecule #1: P2X7 receptor ion channel

SupramoleculeName: P2X7 receptor ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)

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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 norvegicus (Norway rat)
Molecular weightTheoretical: 69.904016 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 PYSNSAVDAG LEVLFQ

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / 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 #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydr...

MacromoleculeName: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine
type: ligand / ID: 7 / Number of copies: 3 / Formula: Q3G
Molecular weightTheoretical: 764.022 Da
Chemical component information

ChemComp-Q3G:
O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine / phospholipid*YM

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Macromolecule #8: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 8 / Number of copies: 18 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 27.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77697
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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