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- PDB-3uu5: The GLIC pentameric Ligand-Gated Ion Channel Loop2-20' mutant red... -

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Basic information

Entry
Database: PDB / ID: 3uu5
TitleThe GLIC pentameric Ligand-Gated Ion Channel Loop2-20' mutant reduced in solution
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Cys-loop receptor family
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / 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
DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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)194,67431
Polymers182,6905
Non-polymers11,98426
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32910 Å2
ΔGint-163 kcal/mol
Surface area62760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.860, 132.980, 160.420
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 11 molecules ABCDE

#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
#4: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 172 molecules

#2: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 5.18 Å3/Da / Density % sol: 76.28 %
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: 0.98011 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: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.9→44.4 Å / Num. all: 82622 / Num. obs: 82457 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 79.74 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.038 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.9-3.060.6372.2119960.3899.9
2.9-44.40.07312.2824570.03899.8

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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: 2.9→44.4 Å / Cor.coef. Fo:Fc: 0.8883 / Cor.coef. Fo:Fc free: 0.8835 / SU R Cruickshank DPI: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.253
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 4113 4.99 %RANDOM
Rwork0.2038 ---
obs0.2045 82450 99.77 %-
Displacement parametersBiso mean: 79.03 Å2
Baniso -1Baniso -2Baniso -3
1--12.2316 Å20 Å229.5851 Å2
2---5.1415 Å20 Å2
3---17.3732 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: LAST / Resolution: 2.9→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 0 352 152 13109
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4622SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes267HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1894HARMONIC5
X-RAY DIFFRACTIONt_it13317HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1762SEMIHARMONIC5
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_contact15441SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13317HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg18122HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.94
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2782 284 4.66 %
Rwork0.2562 5807 -
all0.2572 6091 -
obs--99.77 %

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