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- PDB-4x88: E178D Selectivity filter mutant of NavMS voltage-gated pore -

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Basic information

Entry
Database: PDB / ID: 4x88
TitleE178D Selectivity filter mutant of NavMS voltage-gated pore
ComponentsIon transport proteinIon transporter
KeywordsTRANSPORT PROTEIN / SELECTIVITY FILTER / MEMBRANE PROTEIN
Function / homology
Function and homology information


monoatomic cation channel activity / plasma membrane
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsNaylor, C.E. / Bagneris, C. / Wallace, B.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H01070X United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J020702 United Kingdom
Citation
Journal: Embo J. / Year: 2016
Title: Molecular basis of ion permeability in a voltage-gated sodium channel.
Authors: Naylor, C.E. / Bagneris, C. / DeCaen, P.G. / Sula, A. / Scaglione, A. / Clapham, D.E. / Wallace, B.A.
#1: Journal: Nat Commun / Year: 2013
Title: Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
Authors: Bagneris, C. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W. / Wallace, B.A.
#2: Journal: Nat Commun / Year: 2012
Title: Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
Authors: McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: 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
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
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,85316
Polymers67,2904
Non-polymers2,56312
Water1086
1
A: Ion transport protein
B: Ion transport protein
hetero molecules

A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,85316
Polymers67,2904
Non-polymers2,56312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area9290 Å2
ΔGint-112 kcal/mol
Surface area15930 Å2
MethodPISA
2
C: Ion transport protein
D: Ion transport protein
hetero molecules

C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,85316
Polymers67,2904
Non-polymers2,56312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8750 Å2
ΔGint-88 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.230, 336.020, 80.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

NA

21C-303-

NA

31C-304-

NA

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Components

#1: Protein
Ion transport protein / Ion transporter


Mass: 16822.477 Da / Num. of mol.: 4
Fragment: NavMS pore and C-terminal domain, UNP residues 130-274
Mutation: E178D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus MC-1 (bacteria) / Gene: Mmc1_0798 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0L5S6
#2: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 7.63 Å3/Da / Density % sol: 83.89 % / Description: Flat plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2014
RadiationMonochromator: channe-cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.5→45.93 Å / Num. all: 14189 / Num. obs: 14175 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.251 / Net I/σ(I): 7.7
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZJZ

3zjz


Resolution: 3.5→45.93 Å / Cor.coef. Fo:Fc: 0.8241 / Cor.coef. Fo:Fc free: 0.8693 / SU R Cruickshank DPI: 0.799 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.774 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.328
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 742 5.24 %RANDOM
Rwork0.1977 ---
obs0.198 14163 99.86 %-
Displacement parametersBiso mean: 34.25 Å2
Baniso -1Baniso -2Baniso -3
1-17.6454 Å20 Å20 Å2
2---38.2052 Å20 Å2
3---20.5597 Å2
Refine analyzeLuzzati coordinate error obs: 0.622 Å
Refinement stepCycle: 1 / Resolution: 3.5→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 127 6 2985
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013055HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114152HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d978SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it3055HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion21.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
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_contact3824SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.78 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2103 155 5.43 %
Rwork0.1894 2701 -
all0.1906 2856 -
obs--99.86 %
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)
11.6947-0.60.4713.27290.43352.94450.0517-0.08160.38650.1295-0.1337-0.1594-0.49930.1850.082-0.1469-0.05870.04130.34580.01010.0113-27.7334-63.64611.7935
22.62020.1527-0.40362.7644-0.1291.01250.0312-0.10310.3964-0.1341-0.0571-0.0254-0.32660.29580.02590.0236-0.0353-0.06140.3264-0.0463-0.1093-31.3557-63.688332.2446
31.9320.6644-0.17415.1567-0.36752.96140.0195-0.0112-0.418-0.1453-0.02020.11550.38320.31410.0007-0.10170.0513-0.0780.2850.02450.0125-28.7971-99.495530.1699
41.609-0.87970.8934.26240.1092.15510.0211-0.0444-0.39760.2077-0.0743-0.18240.36240.10890.0533-0.07330.04230.08040.26110.0001-0.1286-29.593-99.67729.2357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|131 - B|220 }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|130 - D|220 }

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