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- PDB-6x9h: Molecular mechanism and structural basis of small-molecule modula... -

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Basic information

Entry
Database: PDB / ID: 6x9h
TitleMolecular mechanism and structural basis of small-molecule modulation of acid-sensing ion channel 1 (ASIC1)
ComponentsAcid-sensing ion channel 1
KeywordsTRANSPORT PROTEIN / ASIC1 / Modulation / MEMBRANE PROTEIN
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
Chem-UZG / Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsLiu, Y. / Ma, J. / DesJarlais, R.L. / Hagan, R. / Rech, J. / Lin, D. / Liu, C. / Miller, R. / Schoellerman, J. / Luo, J. ...Liu, Y. / Ma, J. / DesJarlais, R.L. / Hagan, R. / Rech, J. / Lin, D. / Liu, C. / Miller, R. / Schoellerman, J. / Luo, J. / Letavic, M. / Grasberger, B. / Maher, M.
CitationJournal: Commun Biol / Year: 2021
Title: Molecular mechanism and structural basis of small-molecule modulation of the gating of acid-sensing ion channel 1.
Authors: Liu, Y. / Ma, J. / DesJarlais, R.L. / Hagan, R. / Rech, J. / Lin, D. / Liu, C. / Miller, R. / Schoellerman, J. / Luo, J. / Letavic, M. / Grasberger, B. / Maher, M.
History
DepositionJun 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,31410
Polymers150,4623
Non-polymers1,8527
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-85 kcal/mol
Surface area54840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.786, 116.149, 227.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 50154.086 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1XA76
#2: 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.: 3
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
#3: Chemical ChemComp-UZG / 2-[4-(3,4-dimethoxyphenoxy)phenyl]-1H-benzimidazole-6-carboximidamide


Mass: 388.419 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.52 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM MgCl2, 100 mM HEPES, pH 7.5, 28-30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→35.845 Å / Num. obs: 48207 / % possible obs: 97.85 % / Redundancy: 5 % / Rrim(I) all: 0.169 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 1.708 / Num. unique obs: 4122 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S3W

3s3w


Resolution: 3.01→35.84 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 2280 4.73 %
Rwork0.224 45917 -
obs0.2259 48197 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.32 Å2 / Biso mean: 80.1243 Å2 / Biso min: 29.92 Å2
Refinement stepCycle: final / Resolution: 3.01→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9697 0 130 0 9827
Biso mean--90.71 --
Num. residues----1222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.01-3.070.3878980.37562334243280
3.07-3.140.38261500.32722682283294
3.14-3.220.3941590.31092802296197
3.22-3.310.33321280.29782876300499
3.31-3.410.32021640.28928693033100
3.41-3.520.30821400.266628943034100
3.52-3.640.27761280.252928933021100
3.64-3.790.29111650.215128803045100
3.79-3.960.24981480.200128973045100
3.96-4.170.25651670.202229103077100
4.17-4.430.20661370.181229153052100
4.43-4.770.20361300.157429503080100
4.77-5.250.23081620.169529233085100
5.25-60.21521350.190229583093100
6.01-7.550.28241270.230430203147100
7.56-35.840.25891420.23873114325699

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