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- PDB-7lie: The isolated chicken ASIC1a thumb domain (ATD-c1a) retains the st... -

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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


Stimuli-sensing channels / pH-gated monoatomic ion channel activity / cellular response to pH / ligand-gated sodium channel activity / sodium ion transmembrane transport / postsynaptic membrane / dendrite / 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
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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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

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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 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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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

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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

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