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- PDB-5wkv: Structure of an acid sensing ion channel in a resting state with ... -

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Basic information

Entry
Database: PDB / ID: 5wkv
TitleStructure of an acid sensing ion channel in a resting state with calcium
ComponentsAcid-sensing ion channel 1
KeywordsTRANSPORT PROTEIN / Ion channel / ASIC / ASIC1a / Sodium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / 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
Acid-sensing ion channel domain / acid-sensing ion channel 1 fold / acid-sensing ion channel 1 domain / Acid-sensing ion channels like fold / Acid-sensing ion channels like domains / YojJ-like / Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel ...Acid-sensing ion channel domain / acid-sensing ion channel 1 fold / acid-sensing ion channel 1 domain / Acid-sensing ion channels like fold / Acid-sensing ion channels like domains / YojJ-like / Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: Nature / Year: 2018
Title: Gating mechanisms of acid-sensing ion channels.
Authors: Nate Yoder / Craig Yoshioka / Eric Gouaux /
Abstract: Acid-sensing ion channels (ASICs) are trimeric, proton-gated and sodium-selective members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed ...Acid-sensing ion channels (ASICs) are trimeric, proton-gated and sodium-selective members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout vertebrate central and peripheral nervous systems. Gating of ASICs occurs on a millisecond time scale and the mechanism involves three conformational states: high pH resting, low pH open and low pH desensitized. Existing X-ray structures of ASIC1a describe the conformations of the open and desensitized states, but the structure of the high pH resting state and detailed mechanisms of the activation and desensitization of the channel have remained elusive. Here we present structures of the high pH resting state of homotrimeric chicken (Gallus gallus) ASIC1a, determined by X-ray crystallography and single particle cryo-electron microscopy, and present a comprehensive molecular mechanism for proton-dependent gating in ASICs. In the resting state, the position of the thumb domain is further from the three-fold molecular axis, thereby expanding the 'acidic pocket' in comparison to the open and desensitized states. Activation therefore involves 'closure' of the thumb into the acidic pocket, expansion of the lower palm domain and an iris-like opening of the channel gate. Furthermore, we demonstrate how the β11-β12 linkers that demarcate the upper and lower palm domains serve as a molecular 'clutch', and undergo a simple rearrangement to permit rapid desensitization.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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)152,76817
Polymers150,7233
Non-polymers2,04514
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-139 kcal/mol
Surface area55480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.180, 133.700, 157.650
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.: 2
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 / N-Acetylglucosamine


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 / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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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: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 150 mM NaCl, 19% PEG 1000, 5 mM CaCl2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 37779 / % possible obs: 97.5 % / Redundancy: 5.76 % / CC1/2: 0.979 / Net I/σ(I): 7.05

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Processing

Software
NameVersionClassification
PHENIX(dev_2597: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QTS

2qts


Resolution: 3.2→24.951 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 36.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2971 1877 4.98 %
Rwork0.287 --
obs0.2875 37637 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→24.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9263 0 120 0 9383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039622
X-RAY DIFFRACTIONf_angle_d0.68813144
X-RAY DIFFRACTIONf_dihedral_angle_d12.2615698
X-RAY DIFFRACTIONf_chiral_restr0.0431495
X-RAY DIFFRACTIONf_plane_restr0.0041704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.24380.43251270.4282512X-RAY DIFFRACTION91
3.2438-3.290.44881420.4262601X-RAY DIFFRACTION94
3.29-3.3390.40671300.41952608X-RAY DIFFRACTION93
3.339-3.3910.40821320.42582595X-RAY DIFFRACTION93
3.391-3.44650.43191380.40792598X-RAY DIFFRACTION94
3.4465-3.50580.37331430.40242636X-RAY DIFFRACTION95
3.5058-3.56930.43741360.38972620X-RAY DIFFRACTION95
3.5693-3.63780.47741150.47222094X-RAY DIFFRACTION75
3.6378-3.71180.4718800.50611617X-RAY DIFFRACTION58
3.7118-3.79220.35241340.34662657X-RAY DIFFRACTION95
3.7922-3.88010.37981420.37042643X-RAY DIFFRACTION95
3.8801-3.97680.30691310.32952464X-RAY DIFFRACTION89
3.9768-4.08390.35051490.32192713X-RAY DIFFRACTION96
4.0839-4.20350.29121410.29232695X-RAY DIFFRACTION97
4.2035-4.33850.25161460.27242775X-RAY DIFFRACTION99
4.3385-4.49270.23731450.2492768X-RAY DIFFRACTION99
4.4927-4.67150.23211480.23372747X-RAY DIFFRACTION99
4.6715-4.88260.2131470.22782741X-RAY DIFFRACTION99
4.8826-5.13790.25611450.22712781X-RAY DIFFRACTION99
5.1379-5.45660.2631460.2382769X-RAY DIFFRACTION99
5.4566-5.87290.2741430.26092767X-RAY DIFFRACTION100
5.8729-6.45460.26751470.26292796X-RAY DIFFRACTION100
6.4546-7.36750.27951410.2582769X-RAY DIFFRACTION100
7.3675-9.20410.2721430.22552778X-RAY DIFFRACTION100
9.2041-24.9520.25231460.23612786X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9111-2.37410.53511.5311-2.98494.2052-0.4706-0.21520.13450.62540.4806-0.35250.3952-0.4588-0.17921.3225-0.0022-0.53941.5825-0.0581.223519.7635-8.56921.9402
20.2171-1.4831-0.87941.4922.13438.42070.14421.02550.4525-0.69070.1532-0.0847-0.74110.0636-0.33330.8616-0.1189-0.07352.035-0.06790.8018-13.7274.6984-36.4134
35.64772.69241.12634.9262.57037.9055-0.15690.58230.0288-0.64830.2676-0.1334-0.26890.1182-0.09930.766-0.06180.06141.4992-0.01580.6861-13.46712.2335-17.7944
41.71660.82540.70410.32780.77442.0639-0.1656-0.06770.4915-0.1870.5785-0.78440.02572.85990.00061.0232-0.05330.04062.5906-0.24840.923910.38775.7065-5.0862
54.87992.34311.38140.2205-0.67184.14440.12361.0771-0.8220.03740.1831-0.40490.53221.2372-0.34360.96840.1027-0.02851.696-0.21340.7351-7.3684.6324-21.1021
63.0391-1.22211.07981.3491-0.49862.5444-0.6925-0.68750.26080.4170.5715-0.4947-0.1441-0.83410.20520.983-0.0564-0.16791.6868-0.04021.097118.75061.492216.8467
75.30930.41751.1098-0.8930.99120.086-0.0099-0.70642.6083-0.4518-0.9397-1.2691-0.141-0.45140.77451.1195-0.0508-0.24382.43350.37250.730322.07577.446620.329
84.3627-2.6231.79355.31940.19050.62290.2764-0.17260.6057-0.2384-0.58740.8663-0.1496-1.04980.33931.07080.29870.132.1539-0.14691.2519-39.278419.58483.5861
95.6578-0.35610.41074.1797-1.36566.3382-0.1097-0.94920.14630.2943-0.259-0.0069-0.3297-0.71280.28450.7056-0.11590.0891.3353-0.25650.7002-28.87558.13653.4105
107.16180.6615-1.41211.6794-3.21496.8084-0.7002-0.90342.26271.481.3689-0.43071.1586-1.6438-0.12331.31920.3346-0.64921.543-0.38311.3544-11.53517.910119.314
117.8443-1.08281.26787.733-0.91532.507-1.0772-3.24641.736-0.539-0.2878-2.0169-0.4170.03361.31091.55310.149-0.12861.9386-0.3592.031-24.540232.94959.3008
126.2999-0.18742.7471.04020.28432.885-0.4901-1.95580.30030.26710.1274-0.1721-0.0194-0.43670.32970.8258-0.0083-0.0232.00090.03960.7739-10.05434.13412.6703
132.96681.13990.68971.33631.09292.01290.5358-0.0408-1.29230.1089-0.0771-0.19510.814-0.3706-0.40661.3401-0.0915-0.21521.13130.10041.2371-19.3468-15.11113.8751
146.00550.76041.10196.35661.00754.55530.52410.3677-0.4223-0.14180.10170.15440.5976-0.1026-0.56760.826-0.0978-0.13421.1804-0.11020.6827-22.0708-13.8598-7.0691
156.35932.11141.14444.3561-2.64430.6355-1.1914-2.7955-0.182-1.04170.10261.28570.3345-0.5470.76581.5433-0.5804-0.23091.85280.4091.8102-20.1252-23.10812.9536
165.6444-0.2532.4173.1875-0.00845.79680.2160.4493-0.71520.3005-0.71110.22881.6375-1.66840.45760.9743-0.3756-0.0051.6879-0.26870.7504-17.5872-6.4629-10.5821
174.97110.64532.50981.86970.30575.979-0.20910.66670.8608-0.0418-0.5418-0.12650.43470.64210.66820.7706-0.2386-0.01120.5410.13860.7972-9.9247-7.8889-2.9907
180.5498-0.3585-0.84185.22035.38876.2533-1.54842.0257-0.52251.7222-1.1928-0.18450.8322-0.83661.03221.9331-0.0018-0.3142.56630.15710.974625.5947-5.672543.0988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 42:81)
2X-RAY DIFFRACTION2(chain A and resid 82:163)
3X-RAY DIFFRACTION3(chain A and resid 164:278)
4X-RAY DIFFRACTION4(chain A and resid 279:302)
5X-RAY DIFFRACTION5(chain A and resid 303:407)
6X-RAY DIFFRACTION6(chain A and resid 408:458)
7X-RAY DIFFRACTION7(chain B and resid 42:81)
8X-RAY DIFFRACTION8(chain B and resid 82:205)
9X-RAY DIFFRACTION9(chain B and resid 206:281)
10X-RAY DIFFRACTION10(chain B and resid 282:311)
11X-RAY DIFFRACTION11(chain B and resid 312:359)
12X-RAY DIFFRACTION12(chain B and resid 360:459)
13X-RAY DIFFRACTION13(chain C and resid 42:190)
14X-RAY DIFFRACTION14(chain C and resid 191:278)
15X-RAY DIFFRACTION15(chain C and resid 279:363)
16X-RAY DIFFRACTION16(chain C and resid 364:389)
17X-RAY DIFFRACTION17(chain C and resid 390:435)
18X-RAY DIFFRACTION18(chain C and resid 436:459)

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