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- PDB-5u1l: Crystal structure of the ATP-gated P2X7 ion channel in the closed... -

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Basic information

Entry
Database: PDB / ID: 5u1l
TitleCrystal structure of the ATP-gated P2X7 ion channel in the closed, apo state
ComponentsP2X purinoceptor
KeywordsMEMBRANE PROTEIN / ATP-gated ion channel / no ligand / closed state
Function / homology
Function and homology information


NAD transport / phagolysosome assembly / phospholipid transfer to membrane / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / gamma-aminobutyric acid secretion / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / plasma membrane organization / collagen metabolic process ...NAD transport / phagolysosome assembly / phospholipid transfer to membrane / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / gamma-aminobutyric acid secretion / positive regulation of interleukin-1 alpha production / negative regulation of cell volume / plasma membrane organization / collagen metabolic process / positive regulation of gamma-aminobutyric acid secretion / pore complex assembly / : / positive regulation of prostaglandin secretion / response to fluid shear stress / T cell apoptotic process / ceramide biosynthetic process / bleb assembly / mitochondrial depolarization / vesicle budding from membrane / positive regulation of T cell apoptotic process / glutamate secretion / prostaglandin secretion / cellular response to dsRNA / positive regulation of glutamate secretion / skeletal system morphogenesis / negative regulation of bone resorption / positive regulation of macrophage cytokine production / phospholipid translocation / positive regulation of mitochondrial depolarization / response to ATP / response to zinc ion / negative regulation of MAPK cascade / T cell homeostasis / synaptic vesicle exocytosis / membrane protein ectodomain proteolysis / protein secretion / positive regulation of bone mineralization / T cell proliferation / response to mechanical stimulus / response to electrical stimulus / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / sensory perception of pain / reactive oxygen species metabolic process / mitochondrion organization / positive regulation of interleukin-1 beta production / positive regulation of protein secretion / lipopolysaccharide binding / protein catabolic process / neuromuscular junction / cell morphogenesis / T cell mediated cytotoxicity / protein processing / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / response to calcium ion / MAPK cascade / cell-cell junction / presynapse / postsynapse / response to lipopolysaccharide / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / inflammatory response / positive regulation of protein phosphorylation / external side of plasma membrane / neuronal cell body / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
P2X purinoreceptor 7, intracellular domain / P2X purinoreceptor 7 intracellular domain / P2X7 purinoceptor / atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / ATP P2X receptor / ATP P2X receptors signature. / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily ...P2X purinoreceptor 7, intracellular domain / P2X purinoreceptor 7 intracellular domain / P2X7 purinoceptor / atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / ATP P2X receptor / ATP P2X receptors signature. / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAiluropoda melanoleuca (giant panda)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKarasawa, A. / Kawate, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114379 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS072869 United States
CitationJournal: Elife / Year: 2016
Title: Structural basis for subtype-specific inhibition of the P2X7 receptor.
Authors: Karasawa, A. / Kawate, T.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1593
Polymers38,7161
Non-polymers4422
Water0
1
A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4769
Polymers116,1493
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area9950 Å2
ΔGint-17 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.058, 169.058, 169.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein P2X purinoceptor


Mass: 38716.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Electron density at the N- and C-termini is not well-defined
Source: (gene. exp.) Ailuropoda melanoleuca (giant panda) / Gene: P2RX7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1M6C4
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.6 Å3/Da / Density % sol: 78.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES (pH 7.0), 100 mM NaCl, 4% ethylene glycol, 15% glycerol, 29% PEG-400, 0.1 mg/mL lipid mixture (60% POPE, 20% POPG, and 20% cholesterol).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.1051 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1051 Å / Relative weight: 1
ReflectionResolution: 3.4→48.8 Å / Num. obs: 11207 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 130.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.033 / Rrim(I) all: 0.105 / Net I/σ(I): 16.9 / Num. measured all: 110336
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.67101.3922274122800.7420.4621.4691.799.8
9-48.88.90.032574064410.0110.03359.399.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A740003 bound P2X7

Resolution: 3.4→45.183 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.26
RfactorNum. reflection% reflection
Rfree0.263 1182 10.56 %
Rwork0.2406 --
obs0.2431 11194 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 228.36 Å2 / Biso mean: 125.3547 Å2 / Biso min: 54.03 Å2
Refinement stepCycle: final / Resolution: 3.4→45.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 56 0 2332
Biso mean--186.88 --
Num. residues----317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022361
X-RAY DIFFRACTIONf_angle_d0.4843232
X-RAY DIFFRACTIONf_chiral_restr0.042374
X-RAY DIFFRACTIONf_plane_restr0.003426
X-RAY DIFFRACTIONf_dihedral_angle_d10.1151385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4003-3.55490.3641400.31831226136699
3.5549-3.74230.37091160.297412731389100
3.7423-3.97660.30781560.280412181374100
3.9766-4.28340.34881400.256712531393100
4.2834-4.71410.23961490.190412351384100
4.7141-5.39530.21241590.198612591418100
5.3953-6.79380.2451460.231312611407100
6.7938-45.18660.25251760.254212871463100

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