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- PDB-9e4i: Human ASIC1a at pH 7.5 in complex with MitTx -

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Basic information

Entry
Database: PDB / ID: 9e4i
TitleHuman ASIC1a at pH 7.5 in complex with MitTx
Components
  • Acid-sensing ion channel 1
  • Basic phospholipase A2 homolog MitTx-beta
  • Kunitz-type neurotoxin MitTx-alpha
KeywordsMEMBRANE PROTEIN / Ion channel / Trimer / Toxin
Function / homology
Function and homology information


monoatomic ion-gated channel activity / sensory perception of sour taste / pH-gated monoatomic ion channel activity / cellular response to pH / negative regulation of neurotransmitter secretion / response to acidic pH / ion channel regulator activity / : / neurotransmitter secretion / arachidonate secretion ...monoatomic ion-gated channel activity / sensory perception of sour taste / pH-gated monoatomic ion channel activity / cellular response to pH / negative regulation of neurotransmitter secretion / response to acidic pH / ion channel regulator activity / : / neurotransmitter secretion / arachidonate secretion / ligand-gated sodium channel activity / sodium ion transport / associative learning / regulation of postsynapse assembly / behavioral fear response / lipid catabolic process / phospholipid metabolic process / sodium ion transmembrane transport / response to amphetamine / regulation of membrane potential / serine-type endopeptidase inhibitor activity / postsynaptic density membrane / phospholipid binding / calcium ion transmembrane transport / Stimuli-sensing channels / memory / presynapse / toxin activity / calcium ion binding / dendrite / glutamatergic synapse / cell surface / Golgi apparatus / extracellular region / 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 / Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel / Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily
Similarity search - Domain/homology
Kunitz-type neurotoxin MitTx-alpha / Basic phospholipase A2 homolog MitTx-beta / Acid-sensing ion channel 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Micrurus tener tener (cobra)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsHartfield, K.A. / Yoshioka, C. / Cahill, J. / Baconguis, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138862 United States
CitationJournal: To Be Published
Title: Conformational plasticity of human acid-sensing ion channel 1a
Authors: Cahill, J. / Hartfield, K.A. / Heusser, S.A. / Ritter, N. / Poulsen, M.H. / Yoshioka, C. / Pless, S.A. / Baconguis, I.
History
DepositionOct 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid-sensing ion channel 1
B: Acid-sensing ion channel 1
C: Acid-sensing ion channel 1
D: Kunitz-type neurotoxin MitTx-alpha
E: Basic phospholipase A2 homolog MitTx-beta
F: Kunitz-type neurotoxin MitTx-alpha
G: Basic phospholipase A2 homolog MitTx-beta
H: Kunitz-type neurotoxin MitTx-alpha
I: Basic phospholipase A2 homolog MitTx-beta


Theoretical massNumber of molelcules
Total (without water)243,4159
Polymers243,4159
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Acid-sensing ion channel 1 / ASIC1 / Amiloride-sensitive cation channel 2 / neuronal / Brain sodium channel 2 / BNaC2


Mass: 60252.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Thrombin cleavage product of construct with N-terminal fusion of 8xHis-EGFP-Thrombin site
Source: (gene. exp.) Homo sapiens (human) / Gene: ASIC1, ACCN2, BNAC2 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P78348
#2: Protein Kunitz-type neurotoxin MitTx-alpha


Mass: 7117.976 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Micrurus tener tener (cobra) / References: UniProt: G9I929
#3: Protein Basic phospholipase A2 homolog MitTx-beta / svPLA2 homolog


Mass: 13767.645 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Micrurus tener tener (cobra) / References: UniProt: G9I930
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Homotrimeric complex of acid-sensing channel 1a with three bound MitTx heterodimersCOMPLEXall0MULTIPLE SOURCES
2Homotrimeric complex of human ASIC1aCOMPLEX#11RECOMBINANT
3Heterodimeric complex of MitTx alpha and beta subunitsCOMPLEX#2-#31NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Micrurus tener tener (cobra)1114302
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293S GnTI-
32Homo sapiens (human)9606HEK293S GnTI-
43Homo sapiens (human)9606HEK293S GnTI-
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium phosphateNa2HPO4/NaH2PO41
2200 mMsodium chlorideNaCl1
31 mg/mLdigitonin1
41 mMTris(2-carboxyethyl)phosphine hydrochlorideC9H15O6P1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Monodisperse sample of homotrimeric ASIC1a mixed with MitTx alpha-beta complex
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
8ISOLDEmodel fitting
10PHENIXmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 541317 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214571
ELECTRON MICROSCOPYf_angle_d0.44219707
ELECTRON MICROSCOPYf_dihedral_angle_d4.531962
ELECTRON MICROSCOPYf_chiral_restr0.0372097
ELECTRON MICROSCOPYf_plane_restr0.0032589

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