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- PDB-4fz0: Crystal structure of acid-sensing ion channel in complex with psa... -

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Basic information

Entry
Database: PDB / ID: 4fz0
TitleCrystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at low 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: 2.8 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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid-sensing ion channel 1
B: Acid-sensing ion channel 1
C: Acid-sensing ion channel 1
M: Pi-theraphotoxin-Pc1a
N: Pi-theraphotoxin-Pc1a
O: Pi-theraphotoxin-Pc1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,49516
Polymers168,0996
Non-polymers1,39710
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.290, 108.710, 126.360
Angle α, β, γ (deg.)90.00, 119.78, 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 72:135 or resseq 138:153 or resseq...
211chain B and (resseq 72:135 or resseq 138:153 or resseq...
311chain C and (resseq 72:135 or resseq 138:153 or resseq...
112chain M and (resseq 2:38 )
212chain N and (resseq 2:38 )
312chain O and (resseq 2:38 )

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide / Sugars , 3 types, 11 molecules ABCMNO

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


Mass: 51327.352 Da / Num. of mol.: 3 / Fragment: UNP residues 13-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Production host: HOMO SAPIENS (human) / References: UniProt: Q1XA76
#2: Protein/peptide Pi-theraphotoxin-Pc1a / Pi-TRTX-Pc1a / PcTx1 / Psalmotoxin-1


Mass: 4705.513 Da / Num. of mol.: 3 / Fragment: UNP residues 1-40 / Source method: obtained synthetically / Details: synthetic construct
Source: (synth.) Psalmopoeus cambridgei (Trinidad chevron tarantula)
References: UniProt: P60514
#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.: 5
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 , 3 types, 149 molecules

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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Sodium Acetate, 9-12% PEG 2000 MME, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2011
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 67877 / Num. obs: 63727 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.8→2.85 Å / % possible all: 99.3

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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: 2.8→38.373 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 3195 5.01 %
Rwork0.202 --
obs0.2035 63727 93.2 %
all-67877 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.269 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.6589 Å2-0 Å2-15.3081 Å2
2---12.4711 Å2-0 Å2
3----4.7488 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10328 0 85 144 10557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710686
X-RAY DIFFRACTIONf_angle_d1.1214471
X-RAY DIFFRACTIONf_dihedral_angle_d16.4023879
X-RAY DIFFRACTIONf_chiral_restr0.0771555
X-RAY DIFFRACTIONf_plane_restr0.0051898
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2721X-RAY DIFFRACTIONPOSITIONAL
12B2721X-RAY DIFFRACTIONPOSITIONAL0.082
13C2713X-RAY DIFFRACTIONPOSITIONAL0.073
21M284X-RAY DIFFRACTIONPOSITIONAL
22N284X-RAY DIFFRACTIONPOSITIONAL0.107
23O293X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7849-2.82640.3256710.30021869X-RAY DIFFRACTION67
2.8264-2.87060.29881040.28492280X-RAY DIFFRACTION80
2.8706-2.91760.3611300.28932309X-RAY DIFFRACTION82
2.9176-2.96790.35341130.27382392X-RAY DIFFRACTION84
2.9679-3.02190.27631460.26042406X-RAY DIFFRACTION87
3.0219-3.080.27631390.25662492X-RAY DIFFRACTION89
3.08-3.14280.28661390.24282604X-RAY DIFFRACTION92
3.1428-3.21110.26411330.23342568X-RAY DIFFRACTION92
3.2111-3.28580.28331550.22412632X-RAY DIFFRACTION94
3.2858-3.36790.24611220.20792688X-RAY DIFFRACTION95
3.3679-3.45890.26151510.20532710X-RAY DIFFRACTION96
3.4589-3.56060.23761520.20472726X-RAY DIFFRACTION97
3.5606-3.67540.21681580.18522730X-RAY DIFFRACTION98
3.6754-3.80670.21581530.19242768X-RAY DIFFRACTION98
3.8067-3.9590.20121390.17992771X-RAY DIFFRACTION98
3.959-4.13890.17131270.16352813X-RAY DIFFRACTION99
4.1389-4.35690.17011560.15822801X-RAY DIFFRACTION99
4.3569-4.62940.1591470.15072806X-RAY DIFFRACTION99
4.6294-4.98610.17791550.1582806X-RAY DIFFRACTION99
4.9861-5.48660.23871600.18942806X-RAY DIFFRACTION99
5.4866-6.27760.25031420.2062827X-RAY DIFFRACTION99
6.2776-7.89770.25261670.22312837X-RAY DIFFRACTION100
7.8977-38.37680.26981360.23322891X-RAY DIFFRACTION98

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