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- PDB-3uu3: The GLIC pentameric Ligand-Gated Ion Channel Loop2-20' oxidized m... -

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Basic information

Entry
Database: PDB / ID: 3uu3
TitleThe GLIC pentameric Ligand-Gated Ion Channel Loop2-20' 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: 3.15 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
DepositionNov 28, 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
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)183,2016
Polymers182,6905
Non-polymers5111
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21620 Å2
ΔGint-131 kcal/mol
Surface area64960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.624, 134.234, 160.046
Angle α, β, γ (deg.)90.00, 102.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glr4197 protein / GLIC / ligand-gated ion channel


Mass: 36537.977 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C27S,K33C,T244C
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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.21 Å3/Da / Density % sol: 76.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 15% PEG4000, 0.4 M sodium thiocyanate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.15→44.3 Å / Num. all: 64820 / Num. obs: 64366 / % possible obs: 99.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 93.16 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.043 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.15-3.224.30.6552.193930.35499.5
3.15-44.34.20.07811.5643660.04399.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EAM

3eam


Resolution: 3.15→28.17 Å / Cor.coef. Fo:Fc: 0.9183 / Cor.coef. Fo:Fc free: 0.8939 / SU R Cruickshank DPI: 0.725 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.628 / SU Rfree Blow DPI: 0.359 / SU Rfree Cruickshank DPI: 0.378
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 3198 4.97 %RANDOM
Rwork0.2484 ---
obs0.2496 64282 99.14 %-
Displacement parametersBiso mean: 121.28 Å2
Baniso -1Baniso -2Baniso -3
1--6.6869 Å20 Å221.3194 Å2
2---4.987 Å20 Å2
3---11.6739 Å2
Refine analyzeLuzzati coordinate error obs: 0.916 Å
Refinement stepCycle: LAST / Resolution: 3.15→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12412 0 12 14 12438
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4218SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes250HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1837HARMONIC5
X-RAY DIFFRACTIONt_it12758HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1725SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14960SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12758HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17431HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion20.59
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2679 214 4.51 %
Rwork0.2551 4531 -
all0.2557 4745 -
obs--99.14 %
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)
12.7514-0.15083.18681.8063-0.81165.7247-0.0083-0.06080.1696-0.13010.07550.1904-0.0980.0423-0.06710.26430.0466-0.26290.1895-0.0295-0.046938.9414-7.018930.1942
23.97070.34364.94341.62150.63087.25790.0507-0.0779-0.0714-0.0759-0.00580.258-0.0456-0.0502-0.04490.1494-0.042-0.28490.35530.0325-0.06727.996-29.087135.811
31.79630.39083.03952.70581.37476.71180.0789-0.1546-0.2589-0.2228-0.04330.1710.04970.061-0.03570.13670.0145-0.31040.15960.00940.030143.05-47.850428.2931
41.26740.17092.57052.19310.60967.99180.0148-0.1512-0.1084-0.41490.0441-0.0666-0.00010.1031-0.05890.21090.1033-0.28030.2229-0.0689-0.025263.523-37.469917.6753
51.3462-0.57812.81612.0857-1.2887.8999-0.002-0.11440.108-0.31760.0471-0.0108-0.12470.1491-0.04510.2525-0.1282-0.26290.21080.0321-0.058661.0486-12.256718.9551
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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