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- PDB-4ire: Crystal structure of GLIC with mutations at the loop C region -

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Basic information

Entry
Database: PDB / ID: 4ire
TitleCrystal structure of GLIC with mutations at the loop C region
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / pentameric ligand-gated ion channel / proton-gated ion channel
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / transmembrane transporter complex / 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-LMD / OXALATE ION / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.19 Å
AuthorsChen, Q. / Pan, J. / Liang, Y.H. / Xu, Y. / Tang, P.
CitationJournal: Plos One / Year: 2013
Title: Signal transduction pathways in the pentameric ligand-gated ion channels.
Authors: Mowrey, D. / Chen, Q. / Liang, Y. / Liang, J. / Xu, Y. / Tang, P.
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Structure summary
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Sep 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_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

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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)194,59448
Polymers181,3745
Non-polymers13,22043
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38680 Å2
ΔGint-197 kcal/mol
Surface area61970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.030, 133.620, 161.430
Angle α, β, γ (deg.)90.000, 102.570, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36274.766 Da / Num. of mol.: 5 / Fragment: UNP residues 43-359 / Mutation: D91N, E177Q, D178N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glr4197, glvI / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(de3) Plyss / References: UniProt: Q7NDN8

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Non-polymers , 5 types, 99 molecules

#2: Chemical
ChemComp-LMD / tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside / n-Tetradecyl-b-D-maltopyranosid


Mass: 538.669 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H50O11
#3: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 5.28 Å3/Da / Density % sol: 76.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.9
Details: 10-12% PEG 4000, 225 mM ammonium sulfate, 50 mM sodium acetate buffer (pH 3.9 - 4.1), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2011 / Details: K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.19→30 Å / Num. all: 63002 / Num. obs: 61417 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 88.969 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.07
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.19-3.380.7071.83346479335192.9
3.38-3.610.3923.3351969220197.6
3.61-3.90.2246.06349928760199.4
3.9-4.260.11511.13316768019199.2
4.26-4.750.05917.96270537212197.7
4.75-5.460.04723.4257976465199.2
5.46-6.630.05621.7206555483198.3
6.63-9.160.03233.45162724308198.6
9.16-300.0249.8493562615194.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4F8H

4f8h


Resolution: 3.19→29.857 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.7643 / SU ML: 0.35 / σ(F): 1.99 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 999 1.63 %RANDOM
Rwork0.2039 ---
obs0.2045 61291 97.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.26 Å2 / Biso mean: 88.5796 Å2 / Biso min: 41.75 Å2
Refinement stepCycle: LAST / Resolution: 3.19→29.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12661 0 698 56 13415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913695
X-RAY DIFFRACTIONf_angle_d1.318624
X-RAY DIFFRACTIONf_chiral_restr0.082133
X-RAY DIFFRACTIONf_plane_restr0.0082280
X-RAY DIFFRACTIONf_dihedral_angle_d17.4945374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1904-3.35840.31571330.30388122825593
3.3584-3.56850.25661420.23938533867597
3.5685-3.84350.23781450.18668759890499
3.8435-4.22930.21881450.16068714885999
4.2293-4.83910.19531430.14128625876898
4.8391-6.08820.19871450.20158768891399
6.0882-29.8580.2991460.24038771891798

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