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- PDB-3s3x: Structure of chicken acid-sensing ion channel 1 AT 3.0 A resoluti... -

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Basic information

Entry
Database: PDB / ID: 3s3x
TitleStructure of chicken acid-sensing ion channel 1 AT 3.0 A resolution in complex with psalmotoxin
Components
  • Amiloride-sensitive cation channel 2, neuronal
  • Psalmotoxin-1
KeywordsMEMBRANE PROTEIN / ACID-SENSING / ION CHANNEL / SODIUM CHANNEL / CELL MEMBRANE / GLYCOPROTEIN / ION TRANSPORT / MEMBRANE / SODIUM TRANSPORT / TRANSMEMBRANE / TRANSPORT / TRANSPORT PROTEIN / TOXIN / CYSTEINE KNOT
Function / homology
Function and homology information


: / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / ion channel regulator activity / protein homotrimerization / sodium ion transmembrane transport / toxin activity / extracellular region / 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
: / Psalmotoxin-1 / Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Psalmopoeus cambridgei (Trinidad chevron tarantula)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 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

Downloads & links

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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
D: Psalmotoxin-1
E: Psalmotoxin-1
F: Psalmotoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,44416
Polymers170,9076
Non-polymers1,53710
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20030 Å2
ΔGint-67 kcal/mol
Surface area56630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.396, 109.442, 127.269
Angle α, β, γ (deg.)90.00, 119.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

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...
112chain D and (resseq 2:27 or resseq 29:38 )
212chain E and (resseq 2:27 or resseq 29:38 )
312chain F and (resseq 2:27 or resseq 29:38 )

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide / Sugars , 3 types, 12 molecules ABCDEF

#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: Protein/peptide Psalmotoxin-1 / Pi-TRTX-Pc1a / PcTx1 / Pi-theraphotoxin-Pc1a


Mass: 4346.115 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide
Source: (synth.) Psalmopoeus cambridgei (Trinidad chevron tarantula)
References: UniProt: P60514
#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.: 6
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

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Non-polymers , 4 types, 18 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M sodium acetate pH 5.5, 3 % Glycerol, 3% 1,6-hexanediol, 11 % PEG 6000, 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 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 3→49.03 Å / Num. obs: 55842 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.38 % / Rmerge(I) obs: 0.1083 / Rsym value: 0.1083 / Net I/σ(I): 8.51
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.06 / Rsym value: 0.725 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDS(VERSION May 10data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S3W

3s3w


Resolution: 2.99→29.915 Å / SU ML: 1.01 / σ(F): 1.34 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 2823 5.07 %random
Rwork0.2176 ---
obs0.2192 55678 99.31 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.431 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-24.7524 Å2-0 Å2-25.6394 Å2
2---13.5665 Å2-0 Å2
3----11.186 Å2
Refinement stepCycle: LAST / Resolution: 2.99→29.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10413 0 92 14 10519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410782
X-RAY DIFFRACTIONf_angle_d0.67614544
X-RAY DIFFRACTIONf_dihedral_angle_d11.2844029
X-RAY DIFFRACTIONf_chiral_restr0.041558
X-RAY DIFFRACTIONf_plane_restr0.0031889
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2754X-RAY DIFFRACTIONPOSITIONAL
12B2754X-RAY DIFFRACTIONPOSITIONAL0.053
13C2754X-RAY DIFFRACTIONPOSITIONAL0.072
21D288X-RAY DIFFRACTIONPOSITIONAL
22E288X-RAY DIFFRACTIONPOSITIONAL0.005
23F288X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.04150.51931420.4472621X-RAY DIFFRACTION99
3.0415-3.09680.40511250.4112635X-RAY DIFFRACTION99
3.0968-3.15630.39711340.37022633X-RAY DIFFRACTION99
3.1563-3.22060.38751480.34442628X-RAY DIFFRACTION99
3.2206-3.29060.34791620.31952620X-RAY DIFFRACTION100
3.2906-3.3670.34191220.28382639X-RAY DIFFRACTION99
3.367-3.45110.28131320.2812634X-RAY DIFFRACTION99
3.4511-3.54430.28281200.25622634X-RAY DIFFRACTION99
3.5443-3.64840.27421450.23952638X-RAY DIFFRACTION99
3.6484-3.76590.2591430.23332614X-RAY DIFFRACTION99
3.7659-3.90030.25811380.21352645X-RAY DIFFRACTION99
3.9003-4.05610.20191360.19092638X-RAY DIFFRACTION99
4.0561-4.24020.22011430.17712640X-RAY DIFFRACTION99
4.2402-4.4630.17151580.15662634X-RAY DIFFRACTION99
4.463-4.74160.19091580.15112625X-RAY DIFFRACTION99
4.7416-5.10610.20421470.14822646X-RAY DIFFRACTION100
5.1061-5.61690.20611340.16852677X-RAY DIFFRACTION100
5.6169-6.42260.221380.19662693X-RAY DIFFRACTION99
6.4226-8.06550.26371450.21042649X-RAY DIFFRACTION99
8.0655-29.9170.24281530.22982712X-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)
12.12371.3958-6.88510.5965-1.01464.74940.2306-0.5330.01540.7041-0.4221.0576-0.6470.04340.05741.43970.0240.17221.8133-0.03331.485821.1903-7.01544.0137
22.32320.510.27093.6718-0.08852.0051-0.15550.22030.3588-0.63710.0197-0.2477-0.57470.29250.11180.8302-0.08540.00580.38920.02870.4270.603611.653413.1083
38.00466.36060.29866.644-0.10650.0908-0.0252-0.20321.21730.33780.04651.204-0.1064-0.4781-0.07390.9110.06860.05080.6073-0.05540.699350.455415.088129.5954
41.9916-0.2261-0.09312.62310.85211.25450.0091-0.10590.0260.1786-0.03280.3949-0.0043-0.2663-0.02020.7109-0.0604-0.05820.42880.08570.368356.08744.333822.225
59.0546-5.4428-3.98993.19872.21941.7572-0.47211.747-1.66710.3856-0.49361.73420.0871-1.18391.06351.1795-0.24480.19641.3122-0.16952.022119.9656-12.995226.7771
62.10780.7018-0.17912.8891-0.77174.9461-0.01010.5838-0.2421-0.88080.1445-0.46590.7820.1373-0.06920.91690.0738-0.05250.5114-0.1210.566874.1773-25.40241.4445
72.0467-0.48261.13412.172-0.05782.2665-0.00260.2471-0.1262-0.5433-0.00890.4883-0.0398-0.1677-0.07750.7404-0.0258-0.09780.368-0.01650.46460.332-19.99818.6139
81.11030.613-0.11910.389-0.21610.48420.05570.0318-0.00030.24970.3843-0.3704-0.8341-0.5952-0.43722.1585-0.73090.52272.8276-0.15772.057312.1584-19.167229.6429
95.21691.79570.61410.6599-0.01331.0786-0.33860.2434-0.44740.7736-1.14331.7472-0.4005-1.23981.65641.0999-0.45840.24342.49550.16332.65219.1371-25.74941.0988
101.3928-1.00430.61912.6216-0.21592.18220.0519-0.1989-0.10490.18180.0671-0.06770.15510.0508-0.14430.4207-0.0549-0.04960.3899-0.00620.353777.685-15.930337.8998
112.12582.2609-1.2083.8737-0.71391.9451-0.2647-0.132-0.1345-0.23110.22380.37520.0649-0.3519-0.0550.5149-0.0683-0.06310.51860.07830.343963.1418-6.462632.29
121.73851.302-2.53534.36550.86095.91980.826-0.60690.104-0.26341.20232.08280.0637-1.3544-1.87641.0715-0.33460.23752.14310.49312.372814.2327-17.799946.2433
130.7327-0.6202-1.59558.77571.08673.48410.6156-1.8671.5591.6424-0.7051-0.6085-0.3280.05150.01141.788-0.633-0.5530.6193-0.3150.936276.617529.377342.5247
142.0044-1.86540.3432.39332.57166.5328-0.1452-0.54830.67951.0511-0.0585-0.9513-0.37010.5840.06771.4972-0.2992-0.34530.7874-0.07530.777880.252923.23440.7776
157.73614.87435.29692.00669.08072.00560.1653-1.73510.97361.3102-0.127-0.0922-0.30740.0916-0.01421.8267-0.2287-0.30150.9792-0.19760.722973.81322.086944.7708
169.38961.997-2.10682.00084.69031.99880.2913-0.1103-0.36110.8671-0.15770.03540.42620.0344-0.0040.7279-0.15060.00480.5390.03920.623377.257314.5234.0502
176.2282-1.65465.39412.00366.08282.00410.3836-1.9997-0.3562.4332-1.19810.91421.2766-1.14190.84821.7433-0.18840.05820.9222-0.14810.645670.055919.360643.9996
184.62512.9896-2.25263.291-3.52624.27250.53511.2950.2347-1.67010.00690.0038-0.51570.0487-0.7672.27410.2306-0.07221.1265-0.0490.515558.9406-7.9102-20.1316
192.0021-3.2593-3.52414.2980.27563.42930.10191.64630.5093-1.6506-0.5151-0.23280.02530.6080.42752.32570.1278-0.1491.17920.26460.796362.66150.0251-20.5418
204.9057-6.34447.53889.1881.99752.00210.21781.34220.4481-2.0379-0.71650.7772-0.23820.09440.52891.9832-0.2679-0.16780.92010.15350.593554.3636-3.6953-16.6916
218.7110.6958-5.97038.61883.03051.99960.26980.61130.2255-0.7222-0.2102-0.2518-0.29980.1253-0.04121.5499-0.1309-0.14710.77510.01360.537664.7826-6.205-7.8303
225.14711.10898.39198.00690.18542.0020.31350.77661.0442-0.8706-0.33240.6769-1.6911-1.50980.09371.58370.1549-0.46070.7467-0.0030.723352.1594-4.7619-12.6746
231.09310.15922.56656.0648-1.51886.6309-0.27720.2564-2.7361-0.15910.10050.12051.60990.40870.16641.36580.1146-0.45050.6032-0.01381.23484.5914-48.09437.5074
244.79370.8694-4.64063.38232.58228.12840.2441-0.0066-0.4806-0.82260.7348-0.28270.81980.4329-1.00091.40650.2595-0.36180.5897-0.07081.047885.3493-44.164731.3437
252.0092-9.54613.46052.0045-4.70187.59270.1022-0.693-1.4114-0.86670.4306-0.73681.6764-0.2849-0.51491.22540.197-0.5040.5514-0.05331.312478.1292-46.146132.9799
262.00681.99456.10881.9996-5.49622.00510.36780.6751-0.322-1.15480.004-0.196-0.31260.2096-0.29710.86210.081-0.00060.5836-0.13220.733181.8054-33.541328.399
270.7205-3.33370.47462.003-2.77592.0116-0.26290.8239-1.4536-0.90620.67380.92721.1742-0.8329-0.38831.097-0.208-0.25420.4955-0.0250.907474.1713-43.632233.377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 45:81)
2X-RAY DIFFRACTION2chain 'A' and (resseq 82:282)
3X-RAY DIFFRACTION3chain 'A' and (resseq 283:322)
4X-RAY DIFFRACTION4chain 'A' and (resseq 323:448 or resseq 600
5X-RAY DIFFRACTION5chain 'B' and (resseq 49:81)
6X-RAY DIFFRACTION6chain 'B' and (resseq 82:234)
7X-RAY DIFFRACTION7chain 'B' and (resseq 235:426 or resseq 600
8X-RAY DIFFRACTION8chain 'B' and (resseq 427:449)
9X-RAY DIFFRACTION9chain 'C' and (resseq 50:71)
10X-RAY DIFFRACTION10chain 'C' and (resseq 72:396 or resseq 600 or
11X-RAY DIFFRACTION11chain 'C' and (resseq 397:426)
12X-RAY DIFFRACTION12chain 'C' and (resseq 427:449)
13X-RAY DIFFRACTION13chain 'D' and (resseq 2:6)
14X-RAY DIFFRACTION14chain 'D' and (resseq 7:16)
15X-RAY DIFFRACTION15chain 'D' and (resseq 17:24)
16X-RAY DIFFRACTION16chain 'D' and (resseq 25:31)
17X-RAY DIFFRACTION17chain 'D' and (resseq 32:38)
18X-RAY DIFFRACTION18chain 'E' and (resseq 2:11)
19X-RAY DIFFRACTION19chain 'E' and (resseq 12:16)
20X-RAY DIFFRACTION20chain 'E' and (resseq 17:24)
21X-RAY DIFFRACTION21chain 'E' and (resseq 25:31)
22X-RAY DIFFRACTION22chain 'E' and (resseq 32:38)
23X-RAY DIFFRACTION23chain 'F' and (resseq 2:6)
24X-RAY DIFFRACTION24chain 'F' and (resseq 7:16)
25X-RAY DIFFRACTION25chain 'F' and (resseq 17:24)
26X-RAY DIFFRACTION26chain 'F' and (resseq 25:31)
27X-RAY DIFFRACTION27chain 'F' and (resseq 32:38)

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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