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- PDB-4fz1: Crystal structure of acid-sensing ion channel in complex with psa... -

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Basic information

Entry
Database: PDB / ID: 4fz1
TitleCrystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at high pH
Components
  • Acid-sensing ion channel 1
  • Pi-theraphotoxin-Pc1a
KeywordsTRANSPORT PROTEIN / inhibitor cystine 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: 3.359 Å
AuthorsBaconguis, I. / Gouaux, E.
CitationJournal: Nature / Year: 2012
Title: Structural plasticity and dynamic selectivity of acid-sensing ion channel-spider toxin complexes.
Authors: Baconguis, I. / Gouaux, E.
History
DepositionJul 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
D: Pi-theraphotoxin-Pc1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4754
Polymers56,0332
Non-polymers4422
Water0
1
A: Acid-sensing ion channel 1
D: Pi-theraphotoxin-Pc1a
hetero molecules

A: Acid-sensing ion channel 1
D: Pi-theraphotoxin-Pc1a
hetero molecules

A: Acid-sensing ion channel 1
D: Pi-theraphotoxin-Pc1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,42612
Polymers168,0996
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16090 Å2
ΔGint-65 kcal/mol
Surface area58120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.520, 131.520, 129.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Acid-sensing ion channel 1 / / ASIC1 / Amiloride-sensitive cation channel 2 / neuronal


Mass: 51327.352 Da / Num. of mol.: 1 / Fragment: UNP residues 14-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Cell line (production host): Sf9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q1XA76
#2: Protein/peptide Pi-theraphotoxin-Pc1a / Pi-TRTX-Pc1a / PcTx1 / Psalmotoxin-1


Mass: 4705.513 Da / Num. of mol.: 1 / Fragment: UNP residues 1-40 / Source method: obtained synthetically / Details: synthetic
Source: (synth.) Psalmopoeus cambridgei (Trinidad chevron tarantula)
References: UniProt: P60514
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 20 mM Tris, 14-18% PEG 550 MME, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 11371 / Num. obs: 11369 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.9
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 4 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.4 / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.359→42.823 Å / SU ML: 0.4 / σ(F): 1.97 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 1132 9.96 %
Rwork0.2159 --
obs0.2226 11369 95.25 %
all-11371 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 120.003 Å2 / ksol: 0.253 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.359→42.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 28 0 3203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093288
X-RAY DIFFRACTIONf_angle_d1.2834501
X-RAY DIFFRACTIONf_dihedral_angle_d17.5611096
X-RAY DIFFRACTIONf_chiral_restr0.079509
X-RAY DIFFRACTIONf_plane_restr0.006595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3594-3.51220.30951420.26781263X-RAY DIFFRACTION95
3.5122-3.69730.2841420.27171304X-RAY DIFFRACTION97
3.6973-3.92880.28581440.22651296X-RAY DIFFRACTION96
3.9288-4.23190.29311440.19431281X-RAY DIFFRACTION96
4.2319-4.65730.21051430.16841302X-RAY DIFFRACTION96
4.6573-5.33020.21941370.16441272X-RAY DIFFRACTION96
5.3302-6.71130.33281390.231281X-RAY DIFFRACTION95
6.7113-42.82670.29681410.23491238X-RAY DIFFRACTION92
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)
10.11160.25560.1720.60580.42030.26920.6447-0.3548-0.27110.7419-0.1108-0.16440.5354-0.5272-0.21731.4636-0.0938-0.08651.78150.2272.07599.5005-8.504-6.5774
23.01430.1358-0.58390.763-0.8273.09990.1165-0.2533-0.74580.18010.24041.15231.1753-0.92440.39291.3045-0.2250.02090.8183-0.10411.1041-10.8724-18.234659.9509
31.24890.9258-0.19360.6366-0.41082.5271-0.31730.5763-0.5749-1.31871.00860.26171.1481-0.2602-0.43431.58450.121-0.34621.2154-0.22970.8557-4.99-17.698741.8631
41.60450.20230.05951.02520.31511.2999-0.1384-0.8677-1.19250.9021-0.1766-0.16871.34560.0540.62651.33490.18230.43780.1409-0.13550.1616-6.8161-16.352456.8035
51.0996-0.6591-2.92190.58581.41676.13680.5834-0.6773-0.512-0.25920.4298-0.3598-0.1411.1698-0.76571.1376-0.03480.0261.0651-0.01081.66-4.8065-8.81448.4897
60.07840.01220.00560.06320.01720.366-0.16140.02070.0010.0117-0.1863-0.1021-0.0120.017-0.07621.5441.44120.03241.89260.46512.06414.4284-39.474858.8387
71.41160.7073-0.52940.527-0.06892.48090.44780.4863-0.4741-1.3671-0.68510.1153-0.08890.25540.45432.15640.7348-0.41791.2361-0.01681.506912.1206-29.822957.0752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 41:70 )A41 - 70
2X-RAY DIFFRACTION2( CHAIN A AND RESID 71:258 )A71 - 258
3X-RAY DIFFRACTION3( CHAIN A AND RESID 259:322 )A259 - 322
4X-RAY DIFFRACTION4( CHAIN A AND RESID 323:411 )A323 - 411
5X-RAY DIFFRACTION5( CHAIN A AND RESID 412:450 )A412 - 450
6X-RAY DIFFRACTION6( CHAIN D AND RESID 2:20 )D2 - 20
7X-RAY DIFFRACTION7( CHAIN D AND RESID 21:37 )D21 - 37

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