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- PDB-5xw6: Crystal structure of the chicken ATP-gated P2X7 receptor channel ... -

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Basic information

Entry
Database: PDB / ID: 5xw6
TitleCrystal structure of the chicken ATP-gated P2X7 receptor channel in the presence of competitive antagonist TNP-ATP at 3.1 Angstroms
ComponentsP2X purinoceptor
KeywordsMEMBRANE PROTEIN / Ion channel / Ligand-gated ion channel / P2X receptor / P2X7 receptor / TNP-ATP
Function / homology
Function and homology information


: / : / : / positive regulation of cytokine production => GO:0001819 / Elevation of cytosolic Ca2+ levels / Platelet homeostasis / The NLRP3 inflammasome / response to xenobiotic stimulus => GO:0009410 / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly ...: / : / : / positive regulation of cytokine production => GO:0001819 / Elevation of cytosolic Ca2+ levels / Platelet homeostasis / The NLRP3 inflammasome / response to xenobiotic stimulus => GO:0009410 / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly / plasma membrane => GO:0005886 / NAD transport / phagolysosome assembly / phospholipid transfer to membrane / positive regulation of monoatomic ion transmembrane transport / extracellularly ATP-gated monoatomic cation channel activity / positive regulation of gamma-aminobutyric acid secretion / collagen metabolic process / positive regulation of interleukin-1 alpha production / purinergic nucleotide receptor activity / pore complex assembly / negative regulation of cell volume / positive regulation of prostaglandin secretion / plasma membrane phospholipid scrambling / bleb assembly / vesicle budding from membrane / response to fluid shear stress / cellular response to dsRNA / negative regulation of bone resorption / ceramide biosynthetic process / positive regulation of glutamate secretion / skeletal system morphogenesis / response to zinc ion / response to ATP / positive regulation of mitochondrial depolarization / T cell homeostasis / membrane protein ectodomain proteolysis / response to electrical stimulus / positive regulation of calcium ion transport into cytosol / synaptic vesicle exocytosis / membrane depolarization / T cell proliferation / positive regulation of bone mineralization / response to mechanical stimulus / extrinsic apoptotic signaling pathway / negative regulation of MAPK cascade / release of sequestered calcium ion into cytosol / reactive oxygen species metabolic process / homeostasis of number of cells within a tissue / sensory perception of pain / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / protein catabolic process / neuromuscular junction / mitochondrion organization / lipopolysaccharide binding / protein processing / response to calcium ion / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / cell morphogenesis / cell-cell junction / presynapse / response to lipopolysaccharide / protein phosphorylation / postsynapse / defense response to Gram-positive bacterium / inflammatory response / external side of plasma membrane / neuronal cell body / ATP binding / identical protein binding
Similarity search - Function
atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / P2X7 purinoceptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-128 / P2X purinoceptor
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKasuya, G. / Hattori, M. / Nureki, O.
Funding support Japan, China, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H06294 Japan
Japan Society for the Promotion of Science24227004 Japan
the Ministry of Science and Technology of China2016YFA0502800 China
the National Natural Science Foundation of China31570838 China
the National Natural Science Foundation of China31650110469 China
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel
Authors: Kasuya, G. / Yamaura, T. / Ma, X.B. / Nakamura, R. / Takemoto, M. / Nagumo, H. / Tanaka, E. / Dohmae, N. / Nakane, T. / Yu, Y. / Ishitani, R. / Matsuzaki, O. / Hattori, M. / Nureki, O.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 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
C: P2X purinoceptor
A: P2X purinoceptor
B: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8449
Polymers112,0263
Non-polymers2,8186
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16890 Å2
ΔGint-34 kcal/mol
Surface area45360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.038, 113.038, 333.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNchain AAB27 - 3466 - 325
2ASNASNchain BBC27 - 3466 - 325
3NAGNAGchain CCA - D27 - 5016

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Components

#1: Protein P2X purinoceptor


Mass: 37341.848 Da / Num. of mol.: 3 / Fragment: UNP residues 42-360 / Mutation: N190Q
Source method: isolated from a genetically manipulated source
Details: N190Q mutation / Source: (gene. exp.) Gallus gallus (chicken) / Gene: P2RX7 / Production host: Homo sapiens (human) / References: UniProt: E1C6P3
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#3: Chemical ChemComp-128 / SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE


Type: RNA linking / Mass: 718.270 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H17N8O19P3
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: 4.75 Å3/Da / Density % sol: 74.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.5 M sodium sulfate, 0.05 M lithium chloride, 0.05 M Tris, pH 8.0, 32% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→29.88 Å / Num. obs: 40271 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.097 / Rrim(I) all: 0.242 / Net I/σ(I): 5.2 / Num. measured all: 241339 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.1-3.236.11.3450.6490.5781.468100
11.17-29.885.40.1020.9870.0490.11494.5

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1C

5f1c


Resolution: 3.1→29.88 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.2476 3773 5.08 %
Rwork0.2197 --
obs0.2212 40046 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.26 Å2 / Biso mean: 74.9505 Å2 / Biso min: 26.01 Å2
Refinement stepCycle: final / Resolution: 3.1→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7752 0 180 0 7932
Biso mean--100.54 --
Num. residues----960
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4511X-RAY DIFFRACTION15.416TORSIONAL
12B4511X-RAY DIFFRACTION15.416TORSIONAL
13C4511X-RAY DIFFRACTION15.416TORSIONAL

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