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- PDB-4ntx: Structure of acid-sensing ion channel in complex with snake toxin... -

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Basic information

Entry
Database: PDB / ID: 4ntx
TitleStructure of acid-sensing ion channel in complex with snake toxin and amiloride
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


: / Stimuli-sensing channels / cellular response to pH / ion channel regulator activity / phospholipase A2 activity / arachidonic acid secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process / lipid catabolic process ...: / Stimuli-sensing channels / cellular response to pH / ion channel regulator activity / phospholipase A2 activity / arachidonic acid secretion / protein homotrimerization / sodium ion transmembrane transport / phospholipid metabolic process / lipid catabolic process / serine-type endopeptidase inhibitor activity / toxin activity / 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
Chem-AMR / 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: 2.27 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 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
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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
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
B: Neurotoxin MitTx-alpha
C: Basic phospholipase A2 homolog Tx-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,73113
Polymers72,2133
Non-polymers1,51810
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-54 kcal/mol
Surface area29660 Å2
MethodPISA
2
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)221,19339
Polymers216,6399
Non-polymers4,55430
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 area33880 Å2
ΔGint-226 kcal/mol
Surface area72070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.560, 151.560, 123.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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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Sugars , 1 types, 2 molecules

#4: 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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Non-polymers , 5 types, 188 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-AMR / 3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6-CHLOROPYRAZINECARBOXAMIDE / AMILORIDE / Amiloride


Mass: 229.627 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8ClN7O / Comment: medication*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.77 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM sodium acetate, 22-25% PEG 400, 10 mM magnesium acetate, 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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→29.25 Å / Num. obs: 71494 / % possible obs: 95.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.15 / % possible all: 62

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1402)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29 Å / SU ML: 0.28 / σ(F): 1.44 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 4741 5.02 %Random
Rwork0.2058 ---
obs0.2072 71494 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 96 180 4924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084869
X-RAY DIFFRACTIONf_angle_d1.1376575
X-RAY DIFFRACTIONf_dihedral_angle_d15.1881760
X-RAY DIFFRACTIONf_chiral_restr0.076699
X-RAY DIFFRACTIONf_plane_restr0.005858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.29580.33331490.31472851X-RAY DIFFRACTION91
2.2958-2.32280.3351520.29412825X-RAY DIFFRACTION93
2.3228-2.35120.27981550.29182913X-RAY DIFFRACTION93
2.3512-2.38090.28971550.29382795X-RAY DIFFRACTION93
2.3809-2.41220.30731560.27932934X-RAY DIFFRACTION93
2.4122-2.44520.32641490.28432859X-RAY DIFFRACTION93
2.4452-2.48020.33921570.2812938X-RAY DIFFRACTION94
2.4802-2.51720.28891530.26552865X-RAY DIFFRACTION95
2.5172-2.55650.25581560.26112979X-RAY DIFFRACTION96
2.5565-2.59840.32841550.25552920X-RAY DIFFRACTION96
2.5984-2.64310.29641580.25352996X-RAY DIFFRACTION96
2.6431-2.69120.32481560.24872989X-RAY DIFFRACTION97
2.6912-2.74290.25091560.24822994X-RAY DIFFRACTION97
2.7429-2.79880.28671590.22892992X-RAY DIFFRACTION97
2.7988-2.85960.22531620.21153062X-RAY DIFFRACTION98
2.8596-2.92610.26921590.22683034X-RAY DIFFRACTION98
2.9261-2.99920.24791600.22642987X-RAY DIFFRACTION98
2.9992-3.08020.26691570.22773004X-RAY DIFFRACTION98
3.0802-3.17080.29051570.22553008X-RAY DIFFRACTION98
3.1708-3.2730.22061620.213058X-RAY DIFFRACTION99
3.273-3.38980.28061610.23056X-RAY DIFFRACTION99
3.3898-3.52530.22251610.20453105X-RAY DIFFRACTION99
3.5253-3.68540.20751600.18583064X-RAY DIFFRACTION99
3.6854-3.87930.19771630.18393073X-RAY DIFFRACTION99
3.8793-4.12180.22591600.18143054X-RAY DIFFRACTION100
4.1218-4.4390.16751640.16343115X-RAY DIFFRACTION100
4.439-4.88380.19111620.16213064X-RAY DIFFRACTION100
4.8838-5.58630.17871610.17953061X-RAY DIFFRACTION100
5.5863-7.0220.22231620.19973077X-RAY DIFFRACTION100
7.022-29.250.23271640.20013085X-RAY DIFFRACTION100

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