[English] 日本語
Yorodumi
- PDB-7lie: The isolated chicken ASIC1a thumb domain (ATD-c1a) retains the st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lie
TitleThe isolated chicken ASIC1a thumb domain (ATD-c1a) retains the structure and ligand binding properties of the full length chicken ASIC1a
ComponentsAcid-sensing ion channel 1
KeywordsMEMBRANE PROTEIN / ion channel domain / membrane protein domain / ASIC1a thumb domain
Function / homology
Function and homology information


pH-gated monoatomic ion channel activity / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / protein homotrimerization / sodium ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMishra, B.M. / Mobli, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1162597 Australia
CitationJournal: To Be Published
Title: A reductionist approach for studying the ASIC thumb domain to screen for channel modulators as novel therapeutic leads
Authors: Mishra, B.M. / Mobli, M.
History
DepositionJan 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acid-sensing ion channel 1


Theoretical massNumber of molelcules
Total (without water)8,9221
Polymers8,9221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

-
Components

#1: Protein Acid-sensing ion channel 1 / ASIC1 / Amiloride-sensitive cation channel 2 / neuronal


Mass: 8921.990 Da / Num. of mol.: 1 / Fragment: Thumb domain, residues 291-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1XA76

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D H(CCO)NH
151isotropic13D HNCO
161isotropic13D HBHA(CO)NH
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
191isotropic13D 1H-13C NOESY aromatic
1101isotropic12D 1H-1H NOESY
1111isotropic12D 1H-13C HSQC
1121isotropic13D HN(CA)CO
1131isotropic13D C(CO)NH

-
Sample preparation

DetailsType: solution
Contents: 320 uM [U-100% 13C; U-100% 15N] Thumb domain of the chicken acid-sensing ion channel 1a (cASIC1a), 95% H2O/5% D2O
Details: The freeze-dried ATD-c1a powder was dissolved in 300 uL of 50 mM Bis-Tris buffer pH 7.0 containing 5% D2O, 3 mM sodium azide and 1 mM EDTA. The final concentration of ATD-c1a in solution was 320 uM.
Label: 13C/15N_ATD-c1a / Solvent system: 95% H2O/5% D2O
SampleConc.: 320 uM
Component: Thumb domain of the chicken acid-sensing ion channel 1a (cASIC1a)
Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: Sample was kept at room temperature and pressure / Ionic strength: 50 mM Bis-Tris pH 7.0 mM / Ionic strength err: 0.2 / Label: ATD-c1a / pH: 7.0 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz
Details: The instrument is fitted with a triple-resonance TCI cryoprobe

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.7Bruker Biospincollection
Rowland NMR Toolkit (RNMRTK)3Hoch and Sternprocessing
CcpNmr Analysis2.4.2CCPNpeak picking
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 6 / Details: using automated NOE assignments
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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://pdbjlvh1.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