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- PDB-5wkx: Barium sites in the structure of a resting acid sensing ion channel -

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Basic information

Entry
Database: PDB / ID: 5wkx
TitleBarium sites in the structure of a resting acid sensing ion channel
ComponentsAcid-sensing ion channel 1
KeywordsTRANSPORT PROTEIN / Ion channel / ASIC / ASIC1a / Sodium channel / 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
: / Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.034 Å
AuthorsYoder, N. / Gouaux, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)5T32DK007680 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)5F31NS096782 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)5R01NS038631 United States
CitationJournal: PLoS ONE / Year: 2018
Title: Divalent cation and chloride ion sites of chicken acid sensing ion channel 1a elucidated by x-ray crystallography.
Authors: Yoder, N. / Gouaux, E.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_symm_contact ...pdbx_audit_support / pdbx_validate_symm_contact / struct_conn / struct_site / struct_site_gen
Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: Acid-sensing ion channel 1
B: Acid-sensing ion channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,27612
Polymers150,7233
Non-polymers1,5539
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-106 kcal/mol
Surface area55580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.010, 126.300, 156.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 50241.160 Da / Num. of mol.: 3 / Fragment: UNP residues 25-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Production host: Homo sapiens (human) / References: UniProt: Q1XA76
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 4
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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba

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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: 3.54 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 150 mM NaCl, 29% PEG 400, 20 mM BaCl2. Crystal soaked in 50 mM BaCl2 prior to freezing.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.93725 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.93725 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 33891 / % possible obs: 99.5 % / Redundancy: 6.89 % / CC1/2: 0.999 / Net I/σ(I): 8.82

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Processing

Software
NameVersionClassification
PHENIX(dev_2597: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WKU

5wku


Resolution: 4.034→49.656 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.313 1696 5.02 %
Rwork0.3017 --
obs0.3023 33807 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.034→49.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9267 0 88 0 9355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049596
X-RAY DIFFRACTIONf_angle_d0.70513105
X-RAY DIFFRACTIONf_dihedral_angle_d15.983353
X-RAY DIFFRACTIONf_chiral_restr0.0441485
X-RAY DIFFRACTIONf_plane_restr0.0051702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.034-4.15260.50111320.43112626X-RAY DIFFRACTION97
4.1526-4.28660.41061450.39582666X-RAY DIFFRACTION99
4.2866-4.43970.3671410.35972644X-RAY DIFFRACTION99
4.4397-4.61730.3181440.31252700X-RAY DIFFRACTION99
4.6173-4.82730.26881430.28122673X-RAY DIFFRACTION100
4.8273-5.08160.29111420.27792686X-RAY DIFFRACTION100
5.0816-5.39960.30071370.26722682X-RAY DIFFRACTION100
5.3996-5.81590.30911440.28262691X-RAY DIFFRACTION100
5.8159-6.40010.30251440.30122683X-RAY DIFFRACTION100
6.4001-7.32370.3771370.28592687X-RAY DIFFRACTION100
7.3237-9.21740.22351430.26052698X-RAY DIFFRACTION100
9.2174-49.65970.3241440.31612675X-RAY DIFFRACTION100

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