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- PDB-6u9v: Cryo electron microscopy structure of the ATP-gated rat P2X7 ion ... -

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Basic information

Entry
Database: PDB / ID: 6u9v
TitleCryo electron microscopy structure of the ATP-gated rat P2X7 ion channel in the apo, closed state
ComponentsP2X purinoceptor 7
KeywordsMEMBRANE PROTEIN / Ion Channel Apoptosis
Function / homology
Function and homology information


Platelet homeostasis / The NLRP3 inflammasome / NAD transport / positive regulation of lymphocyte apoptotic process / phospholipid transfer to membrane / regulation of presynaptic dense core granule exocytosis / positive regulation of bleb assembly / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / positive regulation of cytoskeleton organization ...Platelet homeostasis / The NLRP3 inflammasome / NAD transport / positive regulation of lymphocyte apoptotic process / phospholipid transfer to membrane / regulation of presynaptic dense core granule exocytosis / positive regulation of bleb assembly / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / positive regulation of cytoskeleton organization / positive regulation of monoatomic ion transmembrane transport / plasma membrane organization / purinergic nucleotide receptor signaling pathway / positive regulation of prostaglandin secretion / positive regulation of interleukin-1 alpha production / collagen metabolic process / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / bleb assembly / ATP export / positive regulation of catalytic activity / pore complex assembly / negative regulation of cell volume / positive regulation of gamma-aminobutyric acid secretion / plasma membrane phospholipid scrambling / vesicle budding from membrane / programmed cell death / response to fluid shear stress / bleb / negative regulation of bone resorption / ceramide biosynthetic process / cell volume homeostasis / positive regulation of ossification / T cell proliferation / skeletal system morphogenesis / cellular response to dsRNA / phospholipid translocation / response to zinc ion / T cell homeostasis / positive regulation of glutamate secretion / positive regulation of bone mineralization / response to ATP / protein homotrimerization / positive regulation of MAP kinase activity / regulation of sodium ion transport / sodium channel activity / membrane protein ectodomain proteolysis / positive regulation of mitochondrial depolarization / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of calcium ion transport into cytosol / response to electrical stimulus / synaptic vesicle exocytosis / membrane depolarization / homeostasis of number of cells within a tissue / response to mechanical stimulus / monoatomic cation transport / potassium channel activity / extrinsic apoptotic signaling pathway / neuronal action potential / response to bacterium / release of sequestered calcium ion into cytosol / negative regulation of MAPK cascade / reactive oxygen species metabolic process / sensory perception of pain / protein catabolic process / positive regulation of glycolytic process / apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / protein serine/threonine kinase activator activity / mitochondrion organization / neuromuscular junction / lipopolysaccharide binding / protein processing / response to calcium ion / cell morphogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of protein phosphorylation / positive regulation of interleukin-6 production / gene expression / calcium ion transmembrane transport / calcium ion transport / terminal bouton / cell-cell junction / nuclear envelope / response to lipopolysaccharide / channel activity / signaling receptor activity / scaffold protein binding / positive regulation of MAPK cascade / protein phosphorylation / cell surface receptor signaling pathway / postsynapse / defense response to Gram-positive bacterium / response to xenobiotic stimulus / positive regulation of apoptotic process / inflammatory response / copper ion binding / external side of 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
alpha-maltose / GUANOSINE-5'-DIPHOSPHATE / PALMITIC ACID / Chem-Q3G / P2X purinoceptor 7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMansoor, S.E. / McCarthy, A.E.
Funding support United States, 1items
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _database_2.pdbx_DOI ..._atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id

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Structure visualization

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Assembly

Deposited unit
A: P2X purinoceptor 7
B: P2X purinoceptor 7
C: P2X purinoceptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,90651
Polymers209,7123
Non-polymers14,19448
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area45110 Å2
ΔGint-49 kcal/mol
Surface area81090 Å2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein P2X purinoceptor 7


Mass: 69904.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: P2rx7 / Production host: Homo sapiens (human) / References: UniProt: Q64663

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Sugars , 3 types, 18 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 30 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-Q3G / O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine


Mass: 764.022 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H78NO10P / Comment: phospholipid*YM
#8: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C16H32O2

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: P2X7 receptor ion channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77697 / Symmetry type: POINT

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