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- PDB-5heg: Pentameric ligand-gated ion channel GLIC mutant P246G -

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Basic information

Entry
Database: PDB / ID: 5heg
TitlePentameric ligand-gated ion channel GLIC mutant P246G
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / Pentameric ligand-gated ion channels / Membrane protein / Ligand-gated ion channel
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / potassium channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.214 Å
AuthorsBertozzi, C. / Hilf, R.J.C. / Dtuzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Plos Biol. / Year: 2016
Title: Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels.
Authors: Bertozzi, C. / Zimmermann, I. / Engeler, S. / Hilf, R.J. / Dutzler, R.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel


Theoretical massNumber of molelcules
Total (without water)180,9035
Polymers180,9035
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20740 Å2
ΔGint-147 kcal/mol
Surface area66580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.380, 134.210, 160.790
Angle α, β, γ (deg.)90.00, 101.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36180.609 Da / Num. of mol.: 5 / Mutation: P246G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.26 Å3/Da / Density % sol: 76.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: Ammonium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 60901 / % possible obs: 98.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.3
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 9.3 / % possible all: 82.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EHZ

3ehz


Resolution: 3.214→29.924 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 2790 4.6 %
Rwork0.2471 --
obs0.2476 60706 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.214→29.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12590 0 0 0 12590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412925
X-RAY DIFFRACTIONf_angle_d0.77717650
X-RAY DIFFRACTIONf_dihedral_angle_d15.057630
X-RAY DIFFRACTIONf_chiral_restr0.0472055
X-RAY DIFFRACTIONf_plane_restr0.0052210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2144-3.26980.37612896X-RAY DIFFRACTION96
3.2698-3.32920.35363007X-RAY DIFFRACTION99
3.3292-3.39310.33791840.35182855X-RAY DIFFRACTION99
3.3931-3.46230.3781870.34352822X-RAY DIFFRACTION100
3.4623-3.53750.35691550.31182878X-RAY DIFFRACTION100
3.5375-3.61960.3688990.29452954X-RAY DIFFRACTION100
3.6196-3.710.33781190.28412876X-RAY DIFFRACTION100
3.71-3.81010.27761870.27732850X-RAY DIFFRACTION100
3.8101-3.9220.30431870.27372870X-RAY DIFFRACTION100
3.922-4.04830.27021870.25792833X-RAY DIFFRACTION100
4.0483-4.19260.24281400.25362922X-RAY DIFFRACTION100
4.1926-4.360.2804460.22472978X-RAY DIFFRACTION100
4.36-4.55770.25511870.21062844X-RAY DIFFRACTION100
4.5577-4.79710.21041850.18292879X-RAY DIFFRACTION100
4.7971-5.09630.22981870.19552837X-RAY DIFFRACTION100
5.0963-5.48760.26631840.22932852X-RAY DIFFRACTION100
5.4876-6.03570.2464530.24833023X-RAY DIFFRACTION100
6.0357-6.89970.26771340.25052921X-RAY DIFFRACTION100
6.8997-8.65790.28191870.22092909X-RAY DIFFRACTION100
8.6579-29.9250.17921820.2242910X-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)
11.04-0.3549-0.69371.5876-0.00090.61950.0177-0.2036-0.02110.71590.0549-0.1052-0.14210.093200.992-0.09660.0330.77080.07230.670215.3132-5.735577.9331
20.954-0.4266-0.53470.4989-0.07440.42820.3922-0.1535-0.1131-0.0763-0.22780.21830.4475-0.209100.5637-0.09520.0910.7294-0.02180.6371-0.4895-7.622230.6304
31.530.0942-1.09432.33270.15820.9693-0.1292-0.3782-0.05980.40030.0191-0.1447-0.47540.1513-00.74360.0393-0.07020.6731-0.05250.613420.795821.259675.225
40.47110.1257-0.27310.77870.24560.2419-0.1475-0.23820.2917-0.19530.1010.08910.2797-0.385-00.52310.03360.02310.6727-0.03410.6418-1.430613.979131.1069
51.4852-0.7275-0.14680.60850.12580.6572-0.1825-0.12380.17380.23380.2384-0.2404-0.15760.13300.8007-0.0171-0.09330.7114-0.03210.769845.090324.686562.6211
60.94930.6066-0.5420.5516-0.25570.3299-0.37590.2150.2632-0.0494-0.12160.0215-0.75450.0058-0.00470.5997-0.01960.02940.60150.01420.691316.56421.578821.8423
70.9718-0.2911-0.15551.1006-0.66180.92360.1765-0.013-0.0541-0.0986-0.127-0.09680.16380.11800.5527-0.00460.00370.64650.01430.735155.014-0.781557.9836
80.5134-0.0872-0.23430.6226-0.28660.2591-0.15290.02060.0519-0.2035-0.05730.0239-0.11940.2324-00.54670.03780.0480.70530.03580.609628.69924.699215.8424
91.4882-0.1935-0.20111.35280.0410.66330.135-0.2262-0.09220.28340.0335-0.16380.314-0.1161-00.8409-0.0616-0.09780.53970.05360.680236.8816-19.282367.1399
100.130.1296-0.11430.6676-0.55910.27780.07960.1996-0.0999-0.0690.0530.07450.2207-0.021700.60640.03210.03970.5616-0.010.601518.1112-13.329521.2551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 204 )
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 320 )
3X-RAY DIFFRACTION3chain 'B' and (resid 11 through 204 )
4X-RAY DIFFRACTION4chain 'B' and (resid 205 through 320 )
5X-RAY DIFFRACTION5chain 'C' and (resid 11 through 204 )
6X-RAY DIFFRACTION6chain 'C' and (resid 205 through 320 )
7X-RAY DIFFRACTION7chain 'D' and (resid 11 through 204 )
8X-RAY DIFFRACTION8chain 'D' and (resid 205 through 320 )
9X-RAY DIFFRACTION9chain 'E' and (resid 11 through 204 )
10X-RAY DIFFRACTION10chain 'E' and (resid 205 through 320 )

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