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- PDB-3lsv: Structure of the A237F mutant of the pentameric ligand gated ion ... -

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Basic information

Entry
Database: PDB / ID: 3lsv
TitleStructure of the A237F mutant of the pentameric ligand gated ion channel from Gloeobacter Violaceus
ComponentsLigand-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / pLGIC / channel / cys-loop
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
AuthorsNury, H. / Corringer, P.J. / Delarue, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue.
Authors: Nury, H. / Poitevin, F. / Van Renterghem, C. / Changeux, J.P. / Corringer, P.J. / Delarue, M. / Baaden, M.
History
DepositionFeb 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ligand-gated ion channel
B: Ligand-gated ion channel
C: Ligand-gated ion channel
D: Ligand-gated ion channel
E: Ligand-gated ion channel


Theoretical massNumber of molelcules
Total (without water)181,8395
Polymers181,8395
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21880 Å2
ΔGint-152 kcal/mol
Surface area62100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.730, 133.008, 159.898
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ligand-gated ion channel / Glr4197 protein


Mass: 36367.844 Da / Num. of mol.: 5 / Mutation: A279F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q7NDN8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 76.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 4000 ~25%, NaSCN ~400 mM, NaAc ph 4 100 mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3.15→25 Å / Num. obs: 64368 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 79.782 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 10.4
Reflection shellResolution: 3.14→3.15 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER-TNT2.5.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→20.97 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 3192 5.1 %RANDOM
Rwork0.2148 ---
obs0.2153 62602 97.36 %-
Displacement parametersBiso mean: 56.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.11356832 Å20 Å2-0.3972805 Å2
2--1.28952816 Å20 Å2
3----1.17595984 Å2
Refine analyzeLuzzati coordinate error obs: 0.5745 Å
Refinement stepCycle: LAST / Resolution: 3.15→20.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12655 0 0 111 12766
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130002
X-RAY DIFFRACTIONt_angle_deg1.222176802
X-RAY DIFFRACTIONt_dihedral_angle_d21.03923800
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0092602
X-RAY DIFFRACTIONt_gen_planes0.01918755
X-RAY DIFFRACTIONt_it2.6351300020
X-RAY DIFFRACTIONt_nbd0.0622505
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 221 5 %
Rwork0.2669 4196 -
all0.268 4417 -
obs--97.36 %

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