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- PDB-4nty: Cesium sites in the crystal structure of acid-sensing ion channel... -

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Basic information

Entry
Database: PDB / ID: 4nty
TitleCesium sites in the crystal structure of acid-sensing ion channel in complex with snake toxin
Components
  • Acid-sensing ion channel 1
  • Basic phospholipase A2 homolog Tx-beta
  • Neurotoxin MitTx-alpha
KeywordsTRANSPORT PROTEIN/TOXIN / Kunitz / phospholipase A2-like / ion channel / nociception / membrane / TRANSPORT PROTEIN-TOXIN complex
Function / homology
Function and homology information


pH-gated monoatomic ion channel activity / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / ion channel regulator activity / calcium-dependent phospholipase A2 activity / arachidonic acid secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process ...pH-gated monoatomic ion channel activity / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / ion channel regulator activity / calcium-dependent phospholipase A2 activity / arachidonic acid secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process / lipid catabolic process / serine-type endopeptidase inhibitor activity / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / toxin activity / signaling receptor binding / calcium ion binding / 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 / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular / Helix Hairpins / Up-down Bundle / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Kunitz-type neurotoxin MitTx-alpha / Basic phospholipase A2 homolog MitTx-beta / Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Micrurus tener tener (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBaconguis, I. / Bohlen, C.J. / Goehring, A. / Julius, D. / Gouaux, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: X-ray structure of Acid-sensing ion channel 1-snake toxin complex reveals open state of a na(+)-selective channel.
Authors: Baconguis, I. / Bohlen, C.J. / Goehring, A. / Julius, D. / Gouaux, E.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 28, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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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
B: Neurotoxin MitTx-alpha
C: Basic phospholipase A2 homolog Tx-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,59620
Polymers72,2133
Non-polymers2,38317
Water1,58588
1
A: Acid-sensing ion channel 1
B: Neurotoxin MitTx-alpha
C: Basic phospholipase A2 homolog Tx-beta
hetero molecules

A: Acid-sensing ion channel 1
B: Neurotoxin MitTx-alpha
C: Basic phospholipase A2 homolog Tx-beta
hetero molecules

A: Acid-sensing ion channel 1
B: Neurotoxin MitTx-alpha
C: Basic phospholipase A2 homolog Tx-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,78960
Polymers216,6399
Non-polymers7,15051
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area33090 Å2
ΔGint-1032 kcal/mol
Surface area72920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.530, 151.530, 123.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-502-

CS

21A-506-

CS

31A-507-

CS

41A-670-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#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): human embryonic kidney cells / Production host: Homo sapiens (human) / References: UniProt: Q1XA76
#2: Protein Neurotoxin MitTx-alpha


Mass: 7117.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrurus tener tener (cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: G9I929
#3: Protein Basic phospholipase A2 homolog Tx-beta / svPLA2 homolog / MitTx-beta


Mass: 13767.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrurus tener tener (cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: G9I930

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Non-polymers , 4 types, 105 molecules

#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cs
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMODIFIED RESIDUE

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium acetate, 6-9% PEG 4000, pH 5.5, 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: 1.378 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 31004 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.25 / % possible all: 97.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1402)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→46.044 Å / SU ML: 0.33 / σ(F): 1.97 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1476 4.97 %Random
Rwork0.2164 ---
obs0.2184 31004 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→46.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 31 88 4749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084772
X-RAY DIFFRACTIONf_angle_d1.0926457
X-RAY DIFFRACTIONf_dihedral_angle_d14.5971735
X-RAY DIFFRACTIONf_chiral_restr0.071686
X-RAY DIFFRACTIONf_plane_restr0.004846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.68310.30721400.28212551X-RAY DIFFRACTION95
2.6831-2.72710.36361400.28062638X-RAY DIFFRACTION100
2.7271-2.77410.29911400.27652657X-RAY DIFFRACTION100
2.7741-2.82460.32651380.26512716X-RAY DIFFRACTION100
2.8246-2.87890.32721420.24752676X-RAY DIFFRACTION100
2.8789-2.93760.34071380.24512736X-RAY DIFFRACTION100
2.9376-3.00150.26131320.24062672X-RAY DIFFRACTION100
3.0015-3.07130.32911440.24922656X-RAY DIFFRACTION100
3.0713-3.14810.28121440.2472724X-RAY DIFFRACTION100
3.1481-3.23320.31241440.24322678X-RAY DIFFRACTION100
3.2332-3.32830.32151400.24032688X-RAY DIFFRACTION100
3.3283-3.43570.22921480.22362678X-RAY DIFFRACTION100
3.4357-3.55850.29341380.22432697X-RAY DIFFRACTION100
3.5585-3.70090.2421300.20092660X-RAY DIFFRACTION100
3.7009-3.86920.21391460.19392731X-RAY DIFFRACTION100
3.8692-4.07310.20811360.18772645X-RAY DIFFRACTION100
4.0731-4.32810.24241440.18182670X-RAY DIFFRACTION100
4.3281-4.6620.21871380.17712694X-RAY DIFFRACTION100
4.662-5.13060.20061420.17732678X-RAY DIFFRACTION100
5.1306-5.87170.22651380.19482654X-RAY DIFFRACTION100
5.8717-7.39280.24621380.22392709X-RAY DIFFRACTION100
7.3928-46.0440.26091420.24332670X-RAY DIFFRACTION99

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