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- PDB-3s3w: Structure of chicken acid-sensing ion channel 1 at 2.6 a resoluti... -

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Basic information

Entry
Database: PDB / ID: 3s3w
TitleStructure of chicken acid-sensing ion channel 1 at 2.6 a resolution and ph 7.5
ComponentsAmiloride-sensitive cation channel 2, neuronal
KeywordsMEMBRANE PROTEIN / ACID-SENSING / ION CHANNEL / CELL MEMBRANE / GLYCOPROTEIN / ION TRANSPORT / MEMBRANE / SODIUM TRANSPORT / TRANSMEMBRANE / TRANSPORT / TRANSPORT PROTEIN / MEMBRANE GLYCOPROTEIN / SODIUM CHANNEL
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: 2.6 Å
AuthorsDawson, R.J.P. / Benz, J. / Stohler, P. / Tetaz, T. / Joseph, C. / Huber, S. / Schmid, G. / Huegin, D. / Pflimlin, P. / Trube, G. ...Dawson, R.J.P. / Benz, J. / Stohler, P. / Tetaz, T. / Joseph, C. / Huber, S. / Schmid, G. / Huegin, D. / Pflimlin, P. / Trube, G. / Rudolph, M.G. / Hennig, M. / Ruf, A.
CitationJournal: Nat Commun / Year: 2012
Title: Structure of the Acid-sensing ion channel 1 in complex with the gating modifier Psalmotoxin 1.
Authors: Dawson, R.J. / Benz, J. / Stohler, P. / Tetaz, T. / Joseph, C. / Huber, S. / Schmid, G. / Hugin, D. / Pflimlin, P. / Trube, G. / Rudolph, M.G. / Hennig, M. / Ruf, A.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Structure summary
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3May 27, 2015Group: Refinement description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,91212
Polymers157,8693
Non-polymers2,0439
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-71 kcal/mol
Surface area52180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.469, 142.689, 159.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 71:140 or resseq 142:153 or resseq...
211chain B and (resseq 71:140 or resseq 142:153 or resseq...
311chain C and (resseq 71:140 or resseq 142:153 or resseq...

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Components

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


Mass: 52622.848 Da / Num. of mol.: 3 / Fragment: sequence database residues 26-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ACCN2, ASIC1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / 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.: 3
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.: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.99 Å3/Da / Density % sol: 69.15 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris-HCL pH7.5, 0.1M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.6→49 Å / Num. obs: 78139 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.72 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.1566 / Rsym value: 0.1566 / Net I/σ(I): 8.59
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 6.61 % / Rmerge(I) obs: 0.8247 / Mean I/σ(I) obs: 1.18 / Rsym value: 0.8247 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDS(VERSION May 10data reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ij4

3ij4


Resolution: 2.6→47.937 Å / SU ML: 0.94 / σ(F): 1.33 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 3920 5.03 %random
Rwork0.2121 ---
obs0.2132 77969 99.67 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.991 Å2 / ksol: 0.292 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8926 Å2-0 Å2-0 Å2
2---3.0711 Å2-0 Å2
3----0.8215 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9548 0 129 248 9925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039953
X-RAY DIFFRACTIONf_angle_d0.78913442
X-RAY DIFFRACTIONf_dihedral_angle_d14.0593721
X-RAY DIFFRACTIONf_chiral_restr0.0481473
X-RAY DIFFRACTIONf_plane_restr0.0021737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2782X-RAY DIFFRACTIONPOSITIONAL
12B2782X-RAY DIFFRACTIONPOSITIONAL0.042
13C2782X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63170.44051400.4122647X-RAY DIFFRACTION99
2.6317-2.6650.46961290.4092566X-RAY DIFFRACTION99
2.665-2.70010.4361260.39832611X-RAY DIFFRACTION98
2.7001-2.73710.48921450.3752608X-RAY DIFFRACTION100
2.7371-2.77620.35751340.3532599X-RAY DIFFRACTION99
2.7762-2.81760.3781270.32712636X-RAY DIFFRACTION100
2.8176-2.86160.40461370.31842604X-RAY DIFFRACTION100
2.8616-2.90850.35591490.30712620X-RAY DIFFRACTION100
2.9085-2.95870.33061460.27812604X-RAY DIFFRACTION100
2.9587-3.01250.30191570.27412619X-RAY DIFFRACTION100
3.0125-3.07040.28431600.24182602X-RAY DIFFRACTION100
3.0704-3.13310.29121450.24662643X-RAY DIFFRACTION100
3.1331-3.20120.26171310.23422583X-RAY DIFFRACTION100
3.2012-3.27560.25881600.22412640X-RAY DIFFRACTION100
3.2756-3.35750.23381210.21242634X-RAY DIFFRACTION100
3.3575-3.44830.21721340.20852631X-RAY DIFFRACTION99
3.4483-3.54970.24161530.2122638X-RAY DIFFRACTION100
3.5497-3.66420.21091560.20322605X-RAY DIFFRACTION100
3.6642-3.79520.2151450.19552622X-RAY DIFFRACTION99
3.7952-3.9470.20351290.18362666X-RAY DIFFRACTION99
3.947-4.12660.18231140.17192660X-RAY DIFFRACTION100
4.1266-4.3440.16691350.15322666X-RAY DIFFRACTION100
4.344-4.6160.14961330.13552690X-RAY DIFFRACTION100
4.616-4.9720.13071420.13242668X-RAY DIFFRACTION100
4.972-5.47180.18031520.15092694X-RAY DIFFRACTION100
5.4718-6.2620.2561380.19172709X-RAY DIFFRACTION100
6.262-7.88380.24771370.20282737X-RAY DIFFRACTION100
7.8838-47.94490.23111450.24262847X-RAY DIFFRACTION99
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)
11.7885-0.122-1.85013.3147-0.38281.99230.6565-0.4603-1.11630.37720.2065-0.14020.34710.9641-1.52140.6650.0574-0.341.7125-0.07260.831255.812742.438655.7324
21.77660.35830.58252.15591.56153.61420.07550.1673-0.0298-0.1285-0.075-0.1735-0.05460.1651-0.0290.0860.01270.04680.1884-0.01950.152816.922931.75411.4501
32.0402-0.9773-0.79074.76992.16053.0209-0.07120.6401-0.5167-0.6869-0.20860.37490.2401-0.370.17810.3882-0.1063-0.00870.4374-0.07640.24528.815124.8936-3.9568
43.0587-3.3504-1.79346.28474.84744.22760.21060.46580.3583-0.62290.1215-0.6092-0.69620.4135-0.21810.3158-0.06380.09880.35040.06450.295116.971844.79639.3702
52.12370.38690.5672.4131.19362.68-0.01010.1751-0.0826-0.16920.0741-0.2611-0.10460.2692-0.0730.2054-0.00030.02770.21660.00810.145711.307636.118416.4523
61.40953.19852.37617.37835.57834.2613-0.42470.246-0.0239-0.04281.0697-0.83680.02661.8312-0.73330.2898-0.0101-0.01450.6802-0.09340.456534.655831.179820.2633
72.3169-0.32060.09414.4885-0.97547.4136-0.2650.0905-0.3885-0.48890.1757-0.40580.34030.89410.04120.16660.06040.01390.4698-0.11450.381826.420721.00396.2179
81.7788-0.64490.49142.36650.01591.25570.0710.2179-0.0898-0.0218-0.0979-0.1013-0.07740.3609-0.14140.2444-0.01680.03330.32240.02320.155310.845737.379718.0396
92.5765-1.0630.62072.6551-0.31252.6977-0.1769-0.24560.34050.2945-0.0215-0.1967-0.36480.29130.05520.1564-0.05820.04770.16410.02880.051714.432342.877525.6438
101.4478-0.07570.80671.3784-0.22920.47450.045-1.4916-0.32930.49510.2792-0.7588-0.82752.6414-0.44070.9867-0.3408-0.2772.3828-0.36061.257458.264152.188754.9268
111.6921-0.6855-0.23141.3654-0.56521.36010.0363-0.51750.62810.608-0.1509-0.8656-0.40870.88290.01640.4792-0.1258-0.3010.4422-0.14340.596127.030152.281547.9745
123.974-1.0730.91363.6158-0.89543.6492-0.21720.29170.3798-0.4991-0.00720.5446-0.7362-0.35520.14150.3350.1946-0.30610.1341-0.03330.4051-22.190257.371814.8756
131.2962-1.38621.43595.3211-3.39524.2656-0.4216-0.3150.08210.76710.22470.256-0.5706-0.42530.18260.36710.08110.08820.3147-0.09690.3317-12.523748.333539.0285
141.8844-0.55581.65782.4753-0.42662.6802-0.1484-0.04820.10720.0973-0.00750.1042-0.2032-0.06150.20460.15760.02650.04330.1918-0.03780.191-3.796643.62632.3959
155.1376-3.5594.86572.4807-3.55976.5129-0.592-0.92960.76860.27310.1815-0.423-0.6821-0.58620.4210.4856-0.0702-0.1140.3357-0.17190.3158.441563.798137.5105
160.98560.03560.20551.3975-0.56521.3142-0.1315-0.060.1317-0.04240.07180.0315-0.1746-0.02710.08410.22960.0279-0.00310.2324-0.07280.1974-5.401148.561229.9098
170.9271-0.1257-0.47282.17770.13491.59160.4094-0.86340.18851.07970.0758-1.2049-0.57111.1997-0.00180.6734-0.2584-0.37051.0052-0.24950.522337.427656.949755.9054
182.1421.3020.68092.24741.24322.05720.1752-0.4295-0.13150.86160.118-0.75980.00170.6543-0.23940.6133-0.0039-0.29470.6345-0.04620.512332.812241.611855.3423
195.98892.0412-1.97072.3939-1.20732.55720.0355-0.1177-0.3226-0.04380.04780.27850.3735-0.281-0.05050.3288-0.0268-0.06580.15430.02980.2829-8.04369.205636.3944
203.061.03590.24031.4798-0.11711.81160.0267-0.1925-0.16310.1543-0.0363-0.07650.15430.0384-0.01570.2770.0203-0.01980.14050.00410.23584.047421.829933.2618
218.64684.80890.06343.4919-0.44190.33240.6564-1.3599-0.75850.6716-0.5914-0.51910.10960.469-0.1010.57250.0181-0.0930.57010.07550.31759.889122.983356.6218
221.1648-0.0661-0.11841.0633-0.51571.50930.0026-0.3777-0.14360.5129-0.0639-0.28980.01120.252-0.067-0.1802-0.0348-0.3587-0.2877-0.0547-0.488611.21325.768242.3644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 48:71)A48 - 71
2X-RAY DIFFRACTION2chain 'A' and (resseq 72:122)A72 - 122
3X-RAY DIFFRACTION3chain 'A' and (resseq 123:175)A123 - 175
4X-RAY DIFFRACTION4chain 'A' and (resseq 176:208)A176 - 208
5X-RAY DIFFRACTION5chain 'A' and (resseq 209:282)A209 - 282
6X-RAY DIFFRACTION6chain 'A' and (resseq 283:322)A283 - 322
7X-RAY DIFFRACTION7chain 'A' and (resseq 323:354)A323 - 354
8X-RAY DIFFRACTION8chain 'A' and (resseq 355:396 or resseq 600:601 or resseq 700:701)A355 - 396
9X-RAY DIFFRACTION8chain 'A' and (resseq 355:396 or resseq 600:601 or resseq 700:701)A600 - 601
10X-RAY DIFFRACTION8chain 'A' and (resseq 355:396 or resseq 600:601 or resseq 700:701)A700 - 701
11X-RAY DIFFRACTION9chain 'A' and (resseq 397:426)A397 - 426
12X-RAY DIFFRACTION10chain 'A' and (resseq 427:449)A427 - 449
13X-RAY DIFFRACTION11chain 'B' and (resseq 51:95)B51 - 95
14X-RAY DIFFRACTION12chain 'B' and (resseq 96:154)B96 - 154
15X-RAY DIFFRACTION13chain 'B' and (resseq 155:208)B155 - 208
16X-RAY DIFFRACTION14chain 'B' and (resseq 209:282)B209 - 282
17X-RAY DIFFRACTION15chain 'B' and (resseq 283:322)B283 - 322
18X-RAY DIFFRACTION16chain 'B' and (resseq 323:411 or resseq 600:601 or resseq 700:701)B323 - 411
19X-RAY DIFFRACTION16chain 'B' and (resseq 323:411 or resseq 600:601 or resseq 700:701)B600 - 601
20X-RAY DIFFRACTION16chain 'B' and (resseq 323:411 or resseq 600:601 or resseq 700:701)B700 - 701
21X-RAY DIFFRACTION17chain 'B' and (resseq 412:452)B412 - 452
22X-RAY DIFFRACTION18chain 'C' and (resseq 45:95)C45 - 95
23X-RAY DIFFRACTION19chain 'C' and (resseq 96:208)C96 - 208
24X-RAY DIFFRACTION20chain 'C' and (resseq 209:282)C209 - 282
25X-RAY DIFFRACTION21chain 'C' and (resseq 283:322)C283 - 322
26X-RAY DIFFRACTION22chain 'C' and (resseq 323:452 or resseq 600:601 or resseq 700:701)C323 - 452
27X-RAY DIFFRACTION22chain 'C' and (resseq 323:452 or resseq 600:601 or resseq 700:701)C600 - 601
28X-RAY DIFFRACTION22chain 'C' and (resseq 323:452 or resseq 600:601 or resseq 700:701)C700 - 701

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