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- PDB-3ij4: Cesium sites in the crystal structure of a functional acid sensin... -

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Basic information

Entry
Database: PDB / ID: 3ij4
TitleCesium sites in the crystal structure of a functional acid sensing ion channel in the desensitized state
ComponentsAmiloride-sensitive cation channel 2, neuronal
KeywordsTRANSPORT PROTEIN / ACID-SENSING / FUNCTIONAL / ION CHANNEL / TRIMER / MEMBRANE PROTEIN / SODIUM CHANNEL / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Membrane / Sodium / Sodium transport / Transmembrane / Transport / cesium / anomalous
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
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 Å
AuthorsGonzales, E.B. / Gouaux, E.
CitationJournal: Nature / Year: 2009
Title: Pore architecture and ion sites in acid-sensing ion channels and P2X receptors.
Authors: Gonzales, E.B. / Kawate, T. / Gouaux, E.
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amiloride-sensitive cation channel 2, neuronal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6596
Polymers53,0921
Non-polymers5675
Water97354
1
A: Amiloride-sensitive cation channel 2, neuronal
hetero molecules

A: Amiloride-sensitive cation channel 2, neuronal
hetero molecules

A: Amiloride-sensitive cation channel 2, neuronal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,97818
Polymers159,2773
Non-polymers1,70115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17130 Å2
ΔGint-402 kcal/mol
Surface area49520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.787, 131.787, 119.107
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-469-

CS

21A-470-

CS

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Components

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


Mass: 53092.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ACCN2, ASIC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q1XA76
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 150-350 mM NaCl, 100 mM HEPES, 23-28% PEG 400, 10 mM taurine, soaked in 250 mM CsCl cryo solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.3776 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2008
Details: vertically collimating premirror, LN2 cooled double-crystal silicon (111) monochromator, toroidal focusing M2 mirror
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 3→80 Å / Num. obs: 15430 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.095
Reflection shellResolution: 3→3.077 Å / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 1.1 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→27.47 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.723 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.952 / ESU R Free: 0.391
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 794 5.1 %RANDOM
Rwork0.223 ---
obs0.225 14636 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.48 Å2 / Biso mean: 51.848 Å2 / Biso min: 25.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 5 54 3249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223273
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9644449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67424.872156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18615529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9081513
X-RAY DIFFRACTIONr_chiral_restr0.080.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022525
X-RAY DIFFRACTIONr_nbd_refined0.1940.21334
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.215
X-RAY DIFFRACTIONr_mcbond_it0.4071.52077
X-RAY DIFFRACTIONr_mcangle_it0.74223250
X-RAY DIFFRACTIONr_scbond_it0.56231365
X-RAY DIFFRACTIONr_scangle_it0.954.51199
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 66 -
Rwork0.303 1086 -
all-1152 -
obs--100 %

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