[English] 日本語
Yorodumi
- PDB-2rup: Solution structure of rat P2X4 receptor head domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rup
TitleSolution structure of rat P2X4 receptor head domain
ComponentsP2X purinoceptor 4
KeywordsTRANSPORT PROTEIN / P2X4 receptor / head domain / CANION TRANSPORT / METAL ION BINDING
Function / homology
Function and homology information


Platelet homeostasis / ligand-gated monoatomic cation channel activity / Elevation of cytosolic Ca2+ levels / sensory perception of touch / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor signaling pathway / positive regulation of microglial cell migration / negative regulation of cardiac muscle hypertrophy / ligand-gated calcium channel activity ...Platelet homeostasis / ligand-gated monoatomic cation channel activity / Elevation of cytosolic Ca2+ levels / sensory perception of touch / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor signaling pathway / positive regulation of microglial cell migration / negative regulation of cardiac muscle hypertrophy / ligand-gated calcium channel activity / response to fluid shear stress / ATP-gated ion channel activity / regulation of chemotaxis / inorganic cation transmembrane transport / relaxation of cardiac muscle / cellular response to zinc ion / positive regulation of endothelial cell chemotaxis / cellular response to ATP / positive regulation of calcium ion transport into cytosol / response to ATP / behavioral response to pain / membrane depolarization / response to axon injury / neuronal action potential / regulation of cardiac muscle contraction / positive regulation of blood vessel endothelial cell migration / positive regulation of calcium-mediated signaling / regulation of sodium ion transport / monoatomic ion transmembrane transport / sensory perception of pain / nitric oxide biosynthetic process / excitatory postsynaptic potential / response to ischemia / calcium ion transmembrane transport / apoptotic signaling pathway / terminal bouton / regulation of blood pressure / vasodilation / calcium ion transport / apical part of cell / cell junction / cell body / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cadherin binding / copper ion binding / lysosomal membrane / axon / signaling receptor binding / neuronal cell body / dendrite / perinuclear region of cytoplasm / signal transduction / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
P2X4 purinoceptor / ATP P2X receptor / ATP P2X receptors signature. / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsAbe, Y. / Igawa, T. / Tsuda, M. / Inoue, K. / Ueda, T.
CitationJournal: FEBS Lett. / Year: 2015
Title: Solution structure of the rat P2X4 receptor head domain involved in inhibitory metal binding
Authors: Igawa, T. / Abe, Y. / Tsuda, M. / Inoue, K. / Ueda, T.
History
DepositionNov 12, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 11, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P2X purinoceptor 4


Theoretical massNumber of molelcules
Total (without water)6,0671
Polymers6,0671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein P2X purinoceptor 4 / P2X4 / ATP receptor / Purinergic receptor


Mass: 6066.719 Da / Num. of mol.: 1 / Fragment: UNP residues 111-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: P2rx4 / Production host: Escherichia coli (E. coli) / References: UniProt: P51577

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HN(CO)CA
11013D H(CCO)NH
11113D 1H-15N NOESY
11213D 1H-15N TOCSY
11313D (H)CCH-TOCSY
11413D (H)CCH-COSY
11513D 1H-13C NOESY

-
Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] entity-1, 50 mM Urea-2, 10 mM sodium acetate-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-99% 13C; U-99% 15N]1
50 mMUrea-21
10 mMsodium acetate-31
Sample conditionsIonic strength: 0 / pH: 5.0 / Pressure: ambient / Temperature: 297 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1G ntert P.structure solution
CYANA2.1G ntert P.data analysis
CYANA2.1G ntert P.chemical shift assignment
CYANA2.1Cornilescu, Delaglio and Baxstructure solution
CYANA2.1Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Cornilescu, Delaglio and Baxchemical shift assignment
CYANA2.1Hokkaido Universitystructure solution
CYANA2.1Hokkaido Universitydata analysis
CYANA2.1Hokkaido Universitychemical shift assignment
CYANA2.1G ntert P.structure solution
CYANA2.1G ntert P.data analysis
CYANA2.1G ntert P.chemical shift assignment
CYANA2.1Cornilescu, Delaglio and Baxstructure solution
CYANA2.1Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Cornilescu, Delaglio and Baxchemical shift assignment
CYANA2.1Hokkaido Universitystructure solution
CYANA2.1Hokkaido Universitydata analysis
CYANA2.1Hokkaido Universitychemical shift assignment
CYANA2.1G ntert P.structure solution
CYANA2.1G ntert P.data analysis
CYANA2.1G ntert P.chemical shift assignment
CYANA2.1Cornilescu, Delaglio and Baxstructure solution
CYANA2.1Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Cornilescu, Delaglio and Baxchemical shift assignment
CYANA2.1Hokkaido Universitystructure solution
CYANA2.1Hokkaido Universitydata analysis
CYANA2.1Hokkaido Universitychemical shift assignment
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 211 / NOE intraresidue total count: 67 / NOE long range total count: 40 / NOE medium range total count: 22 / NOE sequential total count: 82 / Disulfide bond constraints total count: 3 / Hydrogen bond constraints total count: 11 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 40
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

+
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