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- PDB-5v6n: Crystal Structure of the highly open channel-stabilized mutant C2... -

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Basic information

Entry
Database: PDB / ID: 5v6n
TitleCrystal Structure of the highly open channel-stabilized mutant C27S + K33C + I9'A + N21'C of GLIC under reducing conditions.
ComponentsProton-gated ion channel
Keywordsmembrane protein / metal transport / GLIC / Cys-loop receptors / ion channel / ELIC / GluCl
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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.355 Å
AuthorsGonzalez-Gutierrez, G. / Grosman, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01-NS042169 United States
CitationJournal: J. Gen. Physiol. / Year: 2017
Title: Chasing the open-state structure of pentameric ligand-gated ion channels.
Authors: Gonzalez-Gutierrez, G. / Wang, Y. / Cymes, G.D. / Tajkhorshid, E. / Grosman, C.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Proton-gated ion channel
A: Proton-gated ion channel
B: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,39516
Polymers177,3395
Non-polymers3,05611
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24850 Å2
ΔGint-169 kcal/mol
Surface area63330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.178, 134.063, 159.680
Angle α, β, γ (deg.)90.000, 101.130, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA8 - 319
211chain BB8 - 319
311chain CC8 - 320
411chain DD8 - 319
511chain EE8 - 319

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Components

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


Mass: 35467.805 Da / Num. of mol.: 5 / Fragment: unp residues 50-359 / Mutation: C69S, K75C, I275A, N287C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 5.25 Å3/Da / Density % sol: 76.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200-250 mM (NH4)2SO4, 10-12% (wt/vol) PEG-4000 50 mM sodium acetate, pH 3.9-4.2
PH range: 3.9-4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.355→106.163 Å / Num. obs: 52515 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 68.25 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.095 / Rrim(I) all: 0.262 / Net I/σ(I): 9.6 / Num. measured all: 402323
Reflection shellResolution: 3.355→3.367 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.433 / CC1/2: 0.743 / Rpim(I) all: 0.549 / Rrim(I) all: 1.535 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 3.355→59.76 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.97
RfactorNum. reflection% reflection
Rfree0.2836 2626 5.01 %
Rwork0.2311 --
obs0.2336 52426 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.85 Å2 / Biso mean: 67.7122 Å2 / Biso min: 30.75 Å2
Refinement stepCycle: final / Resolution: 3.355→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12560 0 86 0 12646
Biso mean--65.9 --
Num. residues----1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212975
X-RAY DIFFRACTIONf_angle_d1.62717705
X-RAY DIFFRACTIONf_chiral_restr0.0672055
X-RAY DIFFRACTIONf_plane_restr0.0082205
X-RAY DIFFRACTIONf_dihedral_angle_d14.2724635
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7291X-RAY DIFFRACTION11.638TORSIONAL
12B7291X-RAY DIFFRACTION11.638TORSIONAL
13C7291X-RAY DIFFRACTION11.638TORSIONAL
14D7291X-RAY DIFFRACTION11.638TORSIONAL
15E7291X-RAY DIFFRACTION11.638TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3553-3.41630.37011430.334125822725100
3.4163-3.4820.38841340.313726182752100
3.482-3.55310.34721340.298126012735100
3.5531-3.63040.34231460.284626002746100
3.6304-3.71480.35821550.278326262781100
3.7148-3.80770.29071340.245425892723100
3.8077-3.91060.29631410.247226132754100
3.9106-4.02570.26281390.216626182757100
4.0257-4.15560.25421490.202125962745100
4.1556-4.3040.26731410.209426182759100
4.304-4.47630.28341340.207126232757100
4.4763-4.680.24831190.177126422761100
4.68-4.92660.20231270.168426152742100
4.9266-5.23510.22581340.170126362770100
5.2351-5.6390.23471430.198826332776100
5.639-6.2060.25421330.218526442777100
6.206-7.10270.27421410.230526282769100
7.1027-8.94390.26711440.235126592803100
8.9439-59.76950.33411350.27252659279498

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