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- PDB-4npq: The resting-state conformation of the GLIC ligand-gated ion channel -

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Basic information

Entry
Database: PDB / ID: 4npq
TitleThe resting-state conformation of the GLIC ligand-gated ion channel
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / pentameric ligand-gated ion channel / pH-gated / transmembrane
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
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
Similarity search - Domain/homology
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.35 Å
AuthorsSauguet, L. / Shahsavar, A. / Poitevin, F. / Huon, C. / Menny, A. / Nemecz, A. / Haouz, A. / Changeux, J.P. / Corringer, P.J. / Delarue, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation.
Authors: Sauguet, L. / Shahsavar, A. / Poitevin, F. / Huon, C. / Menny, A. / Nemecz, A. / Haouz, A. / Changeux, J.P. / Corringer, P.J. / Delarue, M.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
F: Proton-gated ion channel
G: Proton-gated ion channel
H: Proton-gated ion channel
I: Proton-gated ion channel
J: Proton-gated ion channel
K: Proton-gated ion channel
L: Proton-gated ion channel
M: Proton-gated ion channel
N: Proton-gated ion channel
O: Proton-gated ion channel
P: Proton-gated ion channel
Q: Proton-gated ion channel
R: Proton-gated ion channel
S: Proton-gated ion channel
T: Proton-gated ion channel


Theoretical massNumber of molelcules
Total (without water)726,97620
Polymers726,97620
Non-polymers00
Water00
1
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


Theoretical massNumber of molelcules
Total (without water)181,7445
Polymers181,7445
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17500 Å2
ΔGint-175 kcal/mol
Surface area69670 Å2
MethodPISA
2
F: Proton-gated ion channel
G: Proton-gated ion channel
H: Proton-gated ion channel
I: Proton-gated ion channel
J: Proton-gated ion channel


Theoretical massNumber of molelcules
Total (without water)181,7445
Polymers181,7445
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16360 Å2
ΔGint-171 kcal/mol
Surface area72540 Å2
MethodPISA
3
K: Proton-gated ion channel
L: Proton-gated ion channel
M: Proton-gated ion channel
N: Proton-gated ion channel
O: Proton-gated ion channel


Theoretical massNumber of molelcules
Total (without water)181,7445
Polymers181,7445
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16960 Å2
ΔGint-166 kcal/mol
Surface area69960 Å2
MethodPISA
4
P: Proton-gated ion channel
Q: Proton-gated ion channel
R: Proton-gated ion channel
S: Proton-gated ion channel
T: Proton-gated ion channel


Theoretical massNumber of molelcules
Total (without water)181,7445
Polymers181,7445
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16190 Å2
ΔGint-159 kcal/mol
Surface area71430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.533, 384.095, 148.439
Angle α, β, γ (deg.)90.00, 98.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36348.805 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Plasmid: pET20B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C43 / References: UniProt: Q7NDN8

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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: 5.1 Å3/Da / Density % sol: 75.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13-15% PEG4000, 200mM KSCN, 10mM CaCl2, 3% Trimethylamine-N-oxyde dihydrate, 0.1M Na Hepes pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 4.35→48.9 Å / Num. all: 96186 / Num. obs: 95802 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 209.37 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.048 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.1 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym value% possible allNum. unique all
4.35-4.591.5810.8999.8
4.6-4.850.83520.47299.811726
4.35-48.940.08410.80.04899.695802

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HFI

4hfi


Resolution: 4.35→20 Å / Cor.coef. Fo:Fc: 0.9242 / Cor.coef. Fo:Fc free: 0.9194 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 4703 5.01 %RANDOM
Rwork0.2401 ---
obs0.2403 93884 99.74 %-
all-94312 --
Displacement parametersBiso mean: 239.13 Å2
Baniso -1Baniso -2Baniso -3
1-21.9969 Å20 Å2-32.861 Å2
2---25.7402 Å20 Å2
3---3.7433 Å2
Refine analyzeLuzzati coordinate error obs: 1.296 Å
Refinement stepCycle: LAST / Resolution: 4.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45859 0 0 0 45859
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00847110HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0264997HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d13906SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes756HARMONIC2
X-RAY DIFFRACTIONt_gen_planes7112HARMONIC5
X-RAY DIFFRACTIONt_it47110HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion21.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion6912SEMIHARMONIC5
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_contact51605SEMIHARMONIC4
LS refinement shellResolution: 4.35→4.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2554 315 4.54 %
Rwork0.253 6630 -
all0.2531 6945 -
obs--99.74 %

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