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- PDB-5u2h: Crystal structure of the ATP-gated P2X7 ion channel bound to ATP ... -

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Basic information

Entry
Database: PDB / ID: 5u2h
TitleCrystal structure of the ATP-gated P2X7 ion channel bound to ATP and allosteric antagonist A804598
ComponentsP2X purinoceptor
KeywordsMEMBRANE PROTEIN / membrane protein: ATP-gated ion channel: agonist and 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-7S1 / ADENOSINE-5'-TRIPHOSPHATE / P2X purinoceptor 7
Similarity search - Component
Biological speciesAiluropoda melanoleuca (giant panda)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.903 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 30, 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_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.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _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_asym_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
B: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6408
Polymers77,4322
Non-polymers2,2086
Water00
1
A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3689
Polymers116,1493
Non-polymers2,2196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8580 Å2
ΔGint-30 kcal/mol
Surface area45650 Å2
MethodPISA
2
B: P2X purinoceptor
hetero molecules

B: P2X purinoceptor
hetero molecules

B: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,55315
Polymers116,1493
Non-polymers4,40412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11560 Å2
ΔGint-35 kcal/mol
Surface area46360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.618, 167.618, 167.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein P2X purinoceptor


Mass: 38716.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N- and C-termini, and several other loop regions 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.: 2
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: Chemical ChemComp-7S1 / N-cyano-N'-[(1R)-1-phenylethyl]-N''-quinolin-5-ylguanidine / antagonist A804598


Mass: 315.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17N5
#4: 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.: 1
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
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
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: 5.06 Å3/Da / Density % sol: 75.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 33% PEG 400, 100 mM MES (pH 6.5), 100 mM NaCl, 5% Glycerol, and 1 mM A804598

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.9→48.39 Å / Num. obs: 14545 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 157.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Rrim(I) all: 0.122 / Net I/σ(I): 15.4 / Num. measured all: 145035
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.9-4.3610.31.0620.877199.9
8.73-48.399.10.0281199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A804598 bound P2X7

Resolution: 3.903→48.387 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3856 1444 9.95 %
Rwork0.334 --
obs0.3372 14511 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.903→48.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 149 0 4116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014211
X-RAY DIFFRACTIONf_angle_d0.4845800
X-RAY DIFFRACTIONf_dihedral_angle_d8.4182416
X-RAY DIFFRACTIONf_chiral_restr0.041695
X-RAY DIFFRACTIONf_plane_restr0.002763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9034-4.04280.41931480.41181255X-RAY DIFFRACTION99
4.0428-4.20460.40621120.37781319X-RAY DIFFRACTION100
4.2046-4.39580.38271440.34271308X-RAY DIFFRACTION100
4.3958-4.62740.38071690.31411262X-RAY DIFFRACTION100
4.6274-4.91710.35251710.32721255X-RAY DIFFRACTION100
4.9171-5.29630.36231520.32741294X-RAY DIFFRACTION100
5.2963-5.82850.36891310.33121316X-RAY DIFFRACTION100
5.8285-6.670.3821620.33751303X-RAY DIFFRACTION100
6.67-8.39640.34621270.33871349X-RAY DIFFRACTION100
8.3964-48.39080.42481280.32321406X-RAY DIFFRACTION100

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