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- PDB-5u1x: Crystal structure of the ATP-gated P2X7 ion channel bound to allo... -

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Basic information

Entry
Database: PDB / ID: 5u1x
TitleCrystal structure of the ATP-gated P2X7 ion channel bound to allosteric antagonist JNJ47965567
ComponentsP2X purinoceptor
KeywordsMEMBRANE PROTEIN / membrane protein: ATP-gated ion channel: allosteric antagonist bound: closed state
Function / homology
Function and homology information


NAD transport / phagolysosome assembly / phospholipid transfer to membrane / gamma-aminobutyric acid secretion / plasma membrane organization / extracellularly ATP-gated monoatomic cation channel activity / pore complex assembly / positive regulation of interleukin-1 alpha production / purinergic nucleotide receptor activity / positive regulation of gamma-aminobutyric acid secretion ...NAD transport / phagolysosome assembly / phospholipid transfer to membrane / gamma-aminobutyric acid secretion / plasma membrane organization / extracellularly ATP-gated monoatomic cation channel activity / pore complex assembly / positive regulation of interleukin-1 alpha production / purinergic nucleotide receptor activity / positive regulation of gamma-aminobutyric acid secretion / negative regulation of cell volume / collagen metabolic process / positive regulation of prostaglandin secretion / T cell apoptotic process / bleb assembly / response to fluid shear stress / mitochondrial depolarization / vesicle budding from membrane / ceramide biosynthetic process / positive regulation of T cell apoptotic process / prostaglandin secretion / cellular response to dsRNA / glutamate secretion / positive regulation of glutamate secretion / negative regulation of bone resorption / positive regulation of macrophage cytokine production / skeletal system morphogenesis / phospholipid translocation / response to zinc ion / response to ATP / positive regulation of mitochondrial depolarization / positive regulation of NLRP3 inflammasome complex assembly / T cell homeostasis / membrane protein ectodomain proteolysis / protein secretion / synaptic vesicle exocytosis / response to electrical stimulus / positive regulation of bone mineralization / response to mechanical stimulus / T cell proliferation / negative regulation of MAPK cascade / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / sensory perception of pain / homeostasis of number of cells within a tissue / reactive oxygen species metabolic process / positive regulation of interleukin-1 beta production / positive regulation of protein secretion / mitochondrion organization / neuromuscular junction / lipopolysaccharide binding / protein catabolic process / T cell mediated cytotoxicity / response to calcium ion / protein processing / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / cell morphogenesis / cell-cell junction / presynapse / MAPK cascade / response to lipopolysaccharide / postsynapse / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / inflammatory response / external side of plasma membrane / neuronal cell body / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / P2X purinoreceptor 7, intracellular domain / P2X purinoreceptor 7 intracellular domain / P2X7 purinoceptor / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor ...atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / 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 / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-7RV / P2X purinoceptor 7
Similarity search - Component
Biological speciesAiluropoda melanoleuca (giant panda)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 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 29, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0725
Polymers38,7161
Non-polymers1,3554
Water00
1
A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,21515
Polymers116,1493
Non-polymers4,06612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area13710 Å2
ΔGint-8 kcal/mol
Surface area45000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.327, 169.327, 169.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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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: Both the N- and C-termini are disordered and the electron density was not well-defined.
Source: (gene. exp.) Ailuropoda melanoleuca (giant panda) / Gene: P2RX7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1M6C4
#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.: 1
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: 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.: 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
#4: Chemical ChemComp-7RV / N-{[4-(4-phenylpiperazin-1-yl)oxan-4-yl]methyl}-2-(phenylsulfanyl)pyridine-3-carboxamide / antagonist JNJ47965567


Mass: 488.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H32N4O2S
Has protein modificationY

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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: 5.22 Å3/Da / Density % sol: 76.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES or Tris (pH 6.0-7.5), 100 mM NaCl, 4% ethylene glycol, 15% glycerol, 27-32% PEG-400 or 31-36% PEG-300, 0.1 mg/mL lipid mixture (60% POPE, 20% POPG, and 20% cholesterol), and 1 mM JNJ-47965567
PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.1→48.88 Å / Num. obs: 14815 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 107.11 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.3110.11.2062698126770.7590.3981.2722.2100
8.77-48.889.40.10265456950.9950.0360.10924.999.3

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A740003 bound P2X7

Resolution: 3.201→48.88 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.66
RfactorNum. reflection% reflection
Rfree0.2642 1394 10.34 %
Rwork0.2217 --
obs0.2258 13483 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.46 Å2 / Biso mean: 103.6362 Å2 / Biso min: 53.9 Å2
Refinement stepCycle: final / Resolution: 3.201→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 91 0 2473
Biso mean--124.05 --
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042540
X-RAY DIFFRACTIONf_angle_d0.7253467
X-RAY DIFFRACTIONf_chiral_restr0.05390
X-RAY DIFFRACTIONf_plane_restr0.005451
X-RAY DIFFRACTIONf_dihedral_angle_d13.7361483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2011-3.31550.36391550.316711951350
3.3155-3.44820.34241450.270611771322
3.4482-3.60510.27291190.261712181337
3.6051-3.79510.34771590.246811731332
3.7951-4.03280.2861400.236112021342
4.0328-4.3440.27421390.199711951334
4.344-4.78080.21951260.161612161342
4.7808-5.47180.21131340.188612241358
5.4718-6.89080.23911450.231512091354
6.8908-48.88620.26821320.234112801412

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