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- PDB-4npp: The GLIC-His10 wild-type structure in equilibrium between the ope... -

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Basic information

Entry
Database: PDB / ID: 4npp
TitleThe GLIC-His10 wild-type structure in equilibrium between the open and locally-closed (LC) forms
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / pentameric ligand-gated ion channel / pH-gated / transmembrane
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / potassium channel activity / 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
NICKEL (II) ION / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 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 ...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_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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)189,23010
Polymers188,9375
Non-polymers2935
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22170 Å2
ΔGint-183 kcal/mol
Surface area63680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.554, 127.618, 185.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37787.305 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q7NDN8
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni

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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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 15-20% PEG2kmme, 50mM NiCl2, 0.1M Na Acetate pH4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.35→48.4 Å / Num. all: 39554 / Num. obs: 39475 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 110.67 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.049 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.35-3.535.11.041.956780.50199.9
3.37-3.535.10.983255930.47499.9
3.35-48.45.20.10112.9394750.04999.8

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Processing

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

4hfi


Resolution: 3.35→19.16 Å / Cor.coef. Fo:Fc: 0.8983 / Cor.coef. Fo:Fc free: 0.8945 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1969 5.02 %RANDOM
Rwork0.2273 ---
obs0.2284 39210 99.82 %-
all-39210 --
Displacement parametersBiso mean: 116.65 Å2
Baniso -1Baniso -2Baniso -3
1--3.7349 Å20 Å20 Å2
2--31.3813 Å20 Å2
3----27.6464 Å2
Refine analyzeLuzzati coordinate error obs: 0.807 Å
Refinement stepCycle: LAST / Resolution: 3.35→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 5 0 12630
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913830HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0218925HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4575SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes275HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1995HARMONIC5
X-RAY DIFFRACTIONt_it13830HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion19.11
X-RAY DIFFRACTIONt_chiral_improper_torsion1895SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15760SEMIHARMONIC4
LS refinement shellResolution: 3.35→3.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3146 135 4.71 %
Rwork0.254 2733 -
all0.2568 2868 -
obs--99.82 %

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