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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/homologyacid-sensing ion channel activity / Epithelial sodium channel, chordates / sensory perception of sour taste / Epithelial sodium channel, conserved site / Epithelial sodium channel / Amiloride-sensitive sodium channels signature. / Amiloride-sensitive sodium channel / Stimuli-sensing channels / negative regulation of neurotransmitter secretion / cellular response to pH ...acid-sensing ion channel activity / Epithelial sodium channel, chordates / sensory perception of sour taste / Epithelial sodium channel, conserved site / Epithelial sodium channel / Amiloride-sensitive sodium channels signature. / Amiloride-sensitive sodium channel / Stimuli-sensing channels / negative regulation of neurotransmitter secretion / cellular response to pH / sodium ion transmembrane transport / response to acidic pH / associative learning / calcium ion transmembrane transport / regulation of membrane potential / protein homotrimerization / memory / synapse / integral component of plasma membrane / Golgi apparatus / identical protein binding / Acid-sensing ion channel 1
Function and homology information
Specimen sourceGallus gallus / bird / Chicken /
MethodX-ray diffraction (3.2 Å resolution / Molecular replacement) / X-ray crystallography
AuthorsYoder, N. / Gouaux, E.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 25, 2017 / Release: Mar 14, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 14, 2018Structure modelrepositoryInitial release
1.1Mar 21, 2018Structure modelDatabase referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Mar 28, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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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)152,80519
Polyers150,7233
Non-polymers2,08116
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15280
ΔGint (kcal/M)-139
Surface area (Å2)55480
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 21

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Components

#1: Protein/peptide 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: (gene. exp.) Gallus gallus / bird / Chicken / / Gene: ASIC1, ACCN2 / Production host: Homo sapiens / References: UniProt:Q1XA76
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 8 / Formula: C8H15NO6 / : N-Acetylglucosamine
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Formula: Cl / : Chloride
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Formula: Ca / : Calcium

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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 / Density percent sol: 67.78
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 24-ID-C / Synchrotron site: APS / Beamline: 24-ID-C / Wavelength: 0.9787
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: Aug 17, 2014
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionD resolution high: 3.2 Å / D resolution low: 100 Å / Number obs: 37779 / CC half: 0.979 / NetI over sigmaI: 7.05 / Redundancy: 5.76 / Percent possible obs: 97.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2597: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QTS
Overall SU ML: 0.67 / Cross valid method: FREE R-VALUE / Sigma F: 1.18 / Overall phase error: 36.52 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2971 / R factor R work: 0.287 / R factor obs: 0.2875 / Highest resolution: 3.2 Å / Lowest resolution: 24.951 Å / Number reflection R free: 1877 / Number reflection obs: 37637 / Percent reflection R free: 4.98 / Percent reflection obs: 94.04
Refine hist #LASTHighest resolution: 3.2 Å / Lowest resolution: 24.951 Å
Number of atoms included #LASTProtein: 9263 / Nucleic acid: 0 / Ligand: 120 / Solvent: 0 / Total: 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
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.20000.43250.42803.2438127251291.00
3.24380.44880.42603.2900142260194.00
3.29000.40670.41953.3390130260893.00
3.33900.40820.42583.3910132259593.00
3.39100.43190.40793.4465138259894.00
3.44650.37330.40243.5058143263695.00
3.50580.43740.38973.5693136262095.00
3.56930.47740.47223.6378115209475.00
3.63780.47180.50613.711880161758.00
3.71180.35240.34663.7922134265795.00
3.79220.37980.37043.8801142264395.00
3.88010.30690.32953.9768131246489.00
3.97680.35050.32194.0839149271396.00
4.08390.29120.29234.2035141269597.00
4.20350.25160.27244.3385146277599.00
4.33850.23730.24904.4927145276899.00
4.49270.23210.23374.6715148274799.00
4.67150.21300.22784.8826147274199.00
4.88260.25610.22715.1379145278199.00
5.13790.26300.23805.4566146276999.00
5.45660.27400.26095.87291432767100.00
5.87290.26750.26296.45461472796100.00
6.45460.27950.25807.36751412769100.00
7.36750.27200.22559.20411432778100.00
9.20410.25230.236124.95201462786100.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.9111-2.37410.53511.5311-2.98494.2052-0.4706-0.21520.13450.62540.4806-0.35250.3952-0.4588-0.17921.3225-0.0022-0.53941.5825-0.05801.223519.7635-8.569021.9402
20.2171-1.4831-0.87941.49202.13438.42070.14421.02550.4525-0.69070.1532-0.0847-0.74110.0636-0.33330.8616-0.1189-0.07352.0350-0.06790.8018-13.72704.6984-36.4134
35.64772.69241.12634.92602.57037.9055-0.15690.58230.0288-0.64830.2676-0.1334-0.26890.1182-0.09930.7660-0.06180.06141.4992-0.01580.6861-13.467012.2335-17.7944
41.71660.82540.70410.32780.77442.0639-0.1656-0.06770.4915-0.18700.5785-0.78440.02572.85990.00061.0232-0.05330.04062.5906-0.24840.923910.38775.7065-5.0862
54.87992.34311.38140.2205-0.67184.14440.12361.0771-0.82200.03740.1831-0.40490.53221.2372-0.34360.96840.1027-0.02851.6960-0.21340.7351-7.36804.6324-21.1021
63.0391-1.22211.07981.3491-0.49862.5444-0.6925-0.68750.26080.41700.5715-0.4947-0.1441-0.83410.20520.9830-0.0564-0.16791.6868-0.04021.097118.75061.492216.8467
75.30930.41751.1098-0.89300.99120.0860-0.0099-0.70642.6083-0.4518-0.9397-1.2691-0.1410-0.45140.77451.1195-0.0508-0.24382.43350.37250.730322.07577.446620.3290
84.3627-2.62301.79355.31940.19050.62290.2764-0.17260.6057-0.2384-0.58740.8663-0.1496-1.04980.33931.07080.29870.13002.1539-0.14691.2519-39.278419.58483.5861
95.6578-0.35610.41074.1797-1.36566.3382-0.1097-0.94920.14630.2943-0.2590-0.0069-0.3297-0.71280.28450.7056-0.11590.08901.3353-0.25650.7002-28.87558.13653.4105
107.16180.6615-1.41211.6794-3.21496.8084-0.7002-0.90342.26271.48001.3689-0.43071.1586-1.6438-0.12331.31920.3346-0.64921.5430-0.38311.3544-11.535017.910119.3140
117.8443-1.08281.26787.7330-0.91532.5070-1.0772-3.24641.7360-0.5390-0.2878-2.0169-0.41700.03361.31091.55310.1490-0.12861.9386-0.35902.0310-24.540232.94959.3008
126.2999-0.18742.74701.04020.28432.8850-0.4901-1.95580.30030.26710.1274-0.1721-0.0194-0.43670.32970.8258-0.0083-0.02302.00090.03960.7739-10.05434.134012.6703
132.96681.13990.68971.33631.09292.01290.5358-0.0408-1.29230.1089-0.0771-0.19510.8140-0.3706-0.40661.3401-0.0915-0.21521.13130.10041.2371-19.3468-15.11113.8751
146.00550.76041.10196.35661.00754.55530.52410.3677-0.4223-0.14180.10170.15440.5976-0.1026-0.56760.8260-0.0978-0.13421.1804-0.11020.6827-22.0708-13.8598-7.0691
156.35932.11141.14444.3561-2.64430.6355-1.1914-2.7955-0.1820-1.04170.10261.28570.3345-0.54700.76581.5433-0.5804-0.23091.85280.40901.8102-20.1252-23.108012.9536
165.6444-0.25302.41703.1875-0.00845.79680.21600.4493-0.71520.3005-0.71110.22881.6375-1.66840.45760.9743-0.3756-0.00501.6879-0.26870.7504-17.5872-6.4629-10.5821
174.97110.64532.50981.86970.30575.9790-0.20910.66670.8608-0.0418-0.5418-0.12650.43470.64210.66820.7706-0.2386-0.01120.54100.13860.7972-9.9247-7.8889-2.9907
180.5498-0.3585-0.84185.22035.38876.2533-1.54842.0257-0.52251.7222-1.1928-0.18450.8322-0.83661.03221.9331-0.0018-0.31402.56630.15710.974625.5947-5.672543.0988
Refine 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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