[English] 日本語
Yorodumi
- PDB-5u2h: Crystal structure of the ATP-gated P2X7 ion channel bound to ATP ... -

+
Open data


ID or keywords:

Loading...

-
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 / pore complex assembly / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / positive regulation of interleukin-1 alpha production / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion ...NAD transport / phagolysosome assembly / phospholipid transfer to membrane / gamma-aminobutyric acid secretion / pore complex assembly / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / positive regulation of interleukin-1 alpha production / plasma membrane organization / positive regulation of gamma-aminobutyric acid secretion / collagen metabolic process / negative regulation of cell volume / T cell apoptotic process / positive regulation of prostaglandin secretion / 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 / positive regulation of glutamate secretion / glutamate secretion / negative regulation of bone resorption / skeletal system morphogenesis / positive regulation of macrophage cytokine production / phospholipid translocation / response to zinc ion / response to ATP / positive regulation of mitochondrial depolarization / positive regulation of NLRP3 inflammasome complex assembly / T cell homeostasis / synaptic vesicle exocytosis / membrane protein ectodomain proteolysis / protein secretion / negative regulation of MAPK cascade / positive regulation of bone mineralization / response to electrical stimulus / response to mechanical stimulus / T cell proliferation / extrinsic apoptotic signaling pathway / homeostasis of number of cells within a tissue / release of sequestered calcium ion into cytosol / sensory perception of pain / reactive oxygen species metabolic process / positive regulation of interleukin-1 beta production / positive regulation of protein secretion / mitochondrion organization / lipopolysaccharide binding / protein catabolic process / T cell mediated cytotoxicity / cell morphogenesis / neuromuscular junction / 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 / response to lipopolysaccharide / postsynapse / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / inflammatory response / response to xenobiotic stimulus / 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 / Purinergic receptor P2X 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more