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- PDB-2xq4: Pentameric ligand gated ion channel GLIC in complex with tetramet... -

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Basic information

Entry
Database: PDB / ID: 2xq4
TitlePentameric ligand gated ion channel GLIC in complex with tetramethylarsonium (TMAs)
ComponentsGLR4197 PROTEIN
KeywordsMEMBRANE PROTEIN / OPEN CHANNEL BLOCK
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / 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
ARSENIC / Proton-gated ion channel
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.6 Å
AuthorsHilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural Basis of Open Channel Block in a Prokaryotic Pentameric Ligand-Gated Ion Channel
Authors: Hilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R.
#1: Journal: Nature / Year: 2009
Title: Structure of a Potentially Open State of a Proton-Activated Pentameric Ligand-Gated Ion Channel.
Authors: Hilf, R.J.C. / Dutzler, R.
History
DepositionSep 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLR4197 PROTEIN
B: GLR4197 PROTEIN
C: GLR4197 PROTEIN
D: GLR4197 PROTEIN
E: GLR4197 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4646
Polymers181,3895
Non-polymers751
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20940 Å2
ΔGint-142.2 kcal/mol
Surface area64280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.314, 128.310, 164.374
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:316 )
211CHAIN B AND (RESSEQ 7:316 )
311CHAIN C AND (RESSEQ 7:316 )
411CHAIN D AND (RESSEQ 7:316 )
511CHAIN E AND (RESSEQ 7:316 )

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Components

#1: Protein
GLR4197 PROTEIN / PENTAMERIC LIGAND GATED ION CHANNEL


Mass: 36277.723 Da / Num. of mol.: 5 / Fragment: RESIDUES 43-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8
#2: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As

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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: 5.31 Å3/Da / Density % sol: 76.67 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 9% PEG 4000, 50 MM CH3COONA, 200 MM (NH4)2SO4, PH 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.045
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 3.4→49.5 Å / Num. obs: 50589 / % possible obs: 89.1 % / Observed criterion σ(I): 2.4 / Redundancy: 1.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.6→40.2 Å / SU ML: 0.39 / σ(F): 1.9 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2722 2151 5.1 %
Rwork0.2592 --
obs0.2599 42598 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.391 Å2 / ksol: 0.269 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-36.2169 Å20 Å2-69.5815 Å2
2---25.4484 Å20 Å2
3----10.7685 Å2
Refinement stepCycle: LAST / Resolution: 3.6→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 0 1 0 12606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112945
X-RAY DIFFRACTIONf_angle_d1.3117685
X-RAY DIFFRACTIONf_dihedral_angle_d17.2654625
X-RAY DIFFRACTIONf_chiral_restr0.0872060
X-RAY DIFFRACTIONf_plane_restr0.0052215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2521X-RAY DIFFRACTIONPOSITIONAL
12B2521X-RAY DIFFRACTIONPOSITIONAL0.056
13C2521X-RAY DIFFRACTIONPOSITIONAL0.048
14D2521X-RAY DIFFRACTIONPOSITIONAL0.051
15E2521X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.595-3.67860.42471270.35782654X-RAY DIFFRACTION98
3.6786-3.77050.36521620.31692656X-RAY DIFFRACTION98
3.7705-3.87240.29781440.30292690X-RAY DIFFRACTION98
3.8724-3.98630.31651370.26772701X-RAY DIFFRACTION99
3.9863-4.11480.29371450.2522673X-RAY DIFFRACTION99
4.1148-4.26170.26021420.25392677X-RAY DIFFRACTION99
4.2617-4.43210.29421330.24922687X-RAY DIFFRACTION99
4.4321-4.63360.24561620.22512680X-RAY DIFFRACTION99
4.6336-4.87750.29511300.212671X-RAY DIFFRACTION98
4.8775-5.18250.21511310.2112679X-RAY DIFFRACTION99
5.1825-5.58160.23771670.22532702X-RAY DIFFRACTION99
5.5816-6.14160.30121640.24992706X-RAY DIFFRACTION100
6.1416-7.02620.2937790.2582803X-RAY DIFFRACTION100
7.0262-8.83670.33041410.23752746X-RAY DIFFRACTION100
8.8367-40.20220.20471870.29072722X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 24.8832 Å / Origin y: -0.5944 Å / Origin z: 52.6507 Å
111213212223313233
T0.2434 Å2-0.0231 Å20.1085 Å2-0.2987 Å20.0012 Å2--0.2314 Å2
L0.3258 °20.0301 °20.4124 °2-0.4199 °20.1102 °2--0.6055 °2
S0.0742 Å °-0.1911 Å °-0.0197 Å °0.2752 Å °-0.043 Å °-0.1126 Å °0.1062 Å °-0.081 Å °0.0039 Å °
Refinement TLS groupSelection details: ALL

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