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- PDB-4il4: The pentameric ligand-gated ion channel GLIC in complex with Se-DDM -

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Basic information

Entry
Database: PDB / ID: 4il4
TitleThe pentameric ligand-gated ion channel GLIC in complex with Se-DDM
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / pentameric ligand-gated ion channel / ion channel / membrane
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
ACETATE ION / Chem-LSM / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSauguet, L. / Malherbe, L. / Corringer, P.J. / Delarue, M.
CitationJournal: Embo J. / Year: 2013
Title: Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.
Authors: Sauguet, L. / Poitevin, F. / Murail, S. / Van Renterghem, C. / Moraga-Cid, G. / Malherbe, L. / Thompson, A.W. / Koehl, P. / Corringer, P.J. / Baaden, M. / Delarue, M.
History
DepositionDec 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Sep 20, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,87734
Polymers181,4595
Non-polymers4,41829
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27360 Å2
ΔGint-280 kcal/mol
Surface area61120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.069, 132.491, 160.219
Angle α, β, γ (deg.)90.00, 102.70, 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
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36291.750 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C43 / References: UniProt: Q7NDN8
#5: Sugar
ChemComp-LSM / dodecyl 4-O-alpha-D-glucopyranosyl-1-seleno-beta-D-glucopyranoside / DODECYL-BETA-D-SELENOMALTOSIDE


Type: D-saccharide / Mass: 573.576 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C24H46O10Se

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Non-polymers , 4 types, 54 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 31 / 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: 5.19 Å3/Da / Density % sol: 76.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 12.5-15% PEG4000, 0.1M NaAcetate pH4, 0.4M NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 55915 / Num. obs: 55635 / % possible obs: 99.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 85.75 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.037 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.3-3.486.30.424.380750.19799.5
3.3-306.10.07715556350.03799.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HFI

4hfi


Resolution: 3.3→29.95 Å / Cor.coef. Fo:Fc: 0.8444 / Cor.coef. Fo:Fc free: 0.8351 / SU R Cruickshank DPI: 1.143 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 2828 5.08 %RANDOM
Rwork0.1952 ---
obs0.1959 55633 99.58 %-
Displacement parametersBiso mean: 87.55 Å2
Baniso -1Baniso -2Baniso -3
1--20.5012 Å20 Å243.7363 Å2
2--1.6611 Å20 Å2
3---18.84 Å2
Refine analyzeLuzzati coordinate error obs: 0.61 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 135 31 12791
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913182HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0817995HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4441SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes270HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1912HARMONIC5
X-RAY DIFFRACTIONt_it13182HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion18.47
X-RAY DIFFRACTIONt_chiral_improper_torsion1776SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact14995SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2443 209 5.15 %
Rwork0.2345 3851 -
all0.235 4060 -
obs--99.58 %

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