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- PDB-3tlu: The GLIC pentameric Ligand-Gated Ion Channel Loop2-24' oxidized m... -

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Basic information

Entry
Database: PDB / ID: 3tlu
TitleThe GLIC pentameric Ligand-Gated Ion Channel Loop2-24' oxidized mutant in a locally-closed conformation (LC1 subtype)
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Cys-loop receptor family
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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSauguet, L. / Nury, H. / Corringer, P.J. / Delarue, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A locally closed conformation of a bacterial pentameric proton-gated ion channel.
Authors: Prevost, M.S. / Sauguet, L. / Nury, H. / Van Renterghem, C. / Huon, C. / Poitevin, F. / Baaden, M. / Delarue, M. / Corringer, P.J.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references

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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)183,23711
Polymers182,5495
Non-polymers6886
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22060 Å2
ΔGint-193 kcal/mol
Surface area63090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.330, 127.810, 159.090
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glr4197 protein / GLIC


Mass: 36509.898 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C69S/K75C/K290C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 4.85 Å3/Da / Density % sol: 74.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4 / Details: pH 4, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.85→47.7 Å / Num. obs: 79676 / % possible obs: 98 % / Redundancy: 5.8 % / Biso Wilson estimate: 69.63 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.053 / Net I/σ(I): 10.9
Reflection shellResolution: 2.85→3 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 2.1 / Num. unique all: 11555 / Rsym value: 0.427 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.1data extraction
SCALAdata scaling
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→44.14 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.8939 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.389 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.357 / SU Rfree Blow DPI: 0.245 / SU Rfree Cruickshank DPI: 0.256
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 3985 5 %RANDOM
Rwork0.2032 ---
obs0.2042 79672 97.81 %-
Displacement parametersBiso max: 231.76 Å2 / Biso mean: 81.0369 Å2 / Biso min: 30.85 Å2
Baniso -1Baniso -2Baniso -3
1--10.053 Å20 Å221.0238 Å2
2---4.7508 Å20 Å2
3---14.8039 Å2
Refine analyzeLuzzati coordinate error obs: 0.411 Å
Refinement stepCycle: LAST / Resolution: 2.85→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12595 0 17 138 12750
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4274SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it12951HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion1760SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15205SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12951HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17715HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion20.61
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2742 287 4.9 %
Rwork0.2557 5568 -
all0.2566 5855 -
obs--97.81 %
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)
10.9638-0.4391.05310.455-0.4811.8530.0043-0.04790.132-0.02150.00610.0688-0.177-0.0781-0.01040.1358-0.0079-0.2242-0.10680.0286-0.08137.7276-7.801230.8138
21.76310.00282.36560.28290.27163.04050.0205-0.1631-0.03730.0225-0.00440.1067-0.0204-0.159-0.016-0.0443-0.0798-0.06810.12150.0446-0.087527.925-30.243236.039
30.76180.11881.37790.55650.47222.70730.0728-0.1026-0.1073-0.0885-0.02160.10230.0686-0.0018-0.05120.1569-0.0434-0.2471-0.13190.0122-0.055143.6913-47.724827.9174
40.42160.07270.74570.51220.21222.05610.01120.0328-0.1125-0.15040.0135-0.08060.05820.2214-0.02470.0885-0.0029-0.1501-0.0061-0.0233-0.110563.6298-35.885717.3472
50.4018-0.02690.88870.425-0.43382.4841-0.03610.00030.0623-0.0846-0.00530.0034-0.06440.1340.04140.13-0.1462-0.218-0.08330.0877-0.083159.9286-11.340619.422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 315
2X-RAY DIFFRACTION2{ B|* }B5 - 315
3X-RAY DIFFRACTION3{ C|* }C5 - 315
4X-RAY DIFFRACTION4{ D|* }D5 - 315
5X-RAY DIFFRACTION5{ E|* }E5 - 315

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