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- PDB-4il9: The pentameric ligand-gated ion channel GLIC A237F in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4il9
TitleThe pentameric ligand-gated ion channel GLIC A237F in complex with bromide
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 / extracellular ligand-gated monoatomic ion channel activity / potassium 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 / BROMIDE ION / DIUNDECYL PHOSPHATIDYL CHOLINE / Unknown ligand / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsSauguet, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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)193,51459
Polymers182,5355
Non-polymers10,97954
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36510 Å2
ΔGint-147 kcal/mol
Surface area62310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.520, 132.140, 159.960
Angle α, β, γ (deg.)90.00, 102.16, 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: 36506.961 Da / Num. of mol.: 5 / Fragment: UNP residues 44-358 / Mutation: A237F
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
#6: 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 , 6 types, 136 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 10 / Source method: obtained synthetically
#5: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br
#7: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 88 / 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: 5.11 Å3/Da
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 12-15% PEG 4K, 0.1M Na Acetate pH 4, 0.2M NaSCN, 0.2M NaBr, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9193 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9193 Å / Relative weight: 1
ReflectionResolution: 2.83→41.8 Å / Num. all: 85708 / Num. obs: 85622 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 63.23 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.055 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.85-30.5932.4124830.37499.4
2.85-41.80.08112.5856220.05599.9

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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: 2.83→41.77 Å / Cor.coef. Fo:Fc: 0.9002 / Cor.coef. Fo:Fc free: 0.8736 / SU R Cruickshank DPI: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 4350 5.01 %RANDOM
Rwork0.2014 ---
obs0.202 -99.23 %-
Displacement parametersBiso mean: 58.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.0002 Å20 Å212.4338 Å2
2---2.2953 Å20 Å2
3---5.2954 Å2
Refine analyzeLuzzati coordinate error obs: 0.356 Å
Refinement stepCycle: LAST / Resolution: 2.83→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12655 0 458 88 13201
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913424HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1218223HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4602SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1910HARMONIC5
X-RAY DIFFRACTIONt_it13424HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion20.09
X-RAY DIFFRACTIONt_chiral_improper_torsion1765SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15125SEMIHARMONIC4
LS refinement shellResolution: 2.83→2.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 275 4.68 %
Rwork0.227 5605 -
all0.2271 5880 -
obs--99.23 %
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)
10.8331-0.15770.6060.6204-0.26351.58380.023-0.03870.07020.0050.04990.0481-0.1743-0.1854-0.07280.00010.0582-0.0653-0.10640.0227-0.104940.081-6.291829.8508
21.78840.10891.55240.44340.20742.39180.08820.032-0.10730.0917-0.00570.10250.0626-0.161-0.0826-0.08180.0132-0.0418-0.03440.0074-0.114527.9788-27.427635.9202
30.850.16780.71940.73330.50892.16970.06380.0669-0.2068-0.0095-0.02940.08290.1314-0.0567-0.0345-0.05290.0144-0.1003-0.1167-0.0405-0.058841.9182-47.045528.944
40.84430.03290.6140.59780.32862.4411-0.00150.123-0.0943-0.1068-0.0064-0.1097-0.11170.13150.0078-0.04580.0236-0.0783-0.1283-0.0445-0.084662.7986-38.106818.0817
50.8427-0.16490.5880.6954-0.44512.40690.02910.05890.1125-0.0985-0.0281-0.1344-0.0767-0.0076-0.001-0.01150.0062-0.0453-0.17020.0151-0.100261.6711-12.996218.7949
60.27930.0360.33890.21690.11140.61820.0384-0.05220.00740.1716-0.0382-0.0946-0.0084-0.0591-0.00020.11720.00060.1354-0.133-0.02250.293858.4406-26.440349.0127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|315 }A5 - 315
2X-RAY DIFFRACTION2{ B|5 - B|315 }B5 - 315
3X-RAY DIFFRACTION3{ C|5 - C|315 }C5 - 315
4X-RAY DIFFRACTION4{ D|5 - D|315 }D5 - 315
5X-RAY DIFFRACTION5{ E|5 - E|315 }E5 - 315
6X-RAY DIFFRACTION6{ A|403 - A|404 C|403 - C|404 B|403 - B|404 E|403 - E|404 D|403 - D|404 }A403 - 404
7X-RAY DIFFRACTION6{ A|403 - A|404 C|403 - C|404 B|403 - B|404 E|403 - E|404 D|403 - D|404 }C403 - 404
8X-RAY DIFFRACTION6{ A|403 - A|404 C|403 - C|404 B|403 - B|404 E|403 - E|404 D|403 - D|404 }B403 - 404
9X-RAY DIFFRACTION6{ A|403 - A|404 C|403 - C|404 B|403 - B|404 E|403 - E|404 D|403 - D|404 }E403 - 404
10X-RAY DIFFRACTION6{ A|403 - A|404 C|403 - C|404 B|403 - B|404 E|403 - E|404 D|403 - D|404 }D403 - 404

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