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- PDB-5hvx: Full length Wild-Type Open-form Sodium Channel NavMs -

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Basic information

Entry
Database: PDB / ID: 5hvx
TitleFull length Wild-Type Open-form Sodium Channel NavMs
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / Integral Membrane Full length Voltage gated sodium channel Transport
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSula, A. / Booker, J.E. / Naylor, C.E. / Wallace, B.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L02625/21 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L006790 United Kingdom
Citation
Journal: Nat Commun / Year: 2017
Title: The complete structure of an activated open sodium channel.
Authors: Sula, A. / Booker, J. / Ng, L.C. / Naylor, C.E. / DeCaen, P.G. / 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.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6679
Polymers31,2201
Non-polymers1,4488
Water1,802100
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,67036
Polymers124,8794
Non-polymers5,79132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area25380 Å2
ΔGint-195 kcal/mol
Surface area49680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.000, 109.000, 210.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-302-

NA

31A-303-

NA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ion transport protein


Mass: 31219.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_0798 / Production host: Escherichia coli (E. coli) / Strain (production host): CD41 / References: UniProt: A0L5S6

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Non-polymers , 6 types, 108 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#4: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 4.9 Å3/Da / Density % sol: 75.01 % / Description: bipyramids
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M NaCl, 0.1 M MES buffer, pH 6.5, 37.8% v/v polyethylene glycol (PEG) 400 and 4% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2015 / Details: bi-morph mirrors
RadiationMonochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 69.99 Å2
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 29.3 % / Rmerge(I) obs: 2.57 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSOct 15, 2015data reduction
XDSOct, 15, 2015data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rvy

3rvy


Resolution: 2.45→27.67 Å / Cor.coef. Fo:Fc: 0.9214 / Cor.coef. Fo:Fc free: 0.9097 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1232 5.19 %RANDOM
Rwork0.2073 ---
obs0.2087 23759 99.99 %-
Displacement parametersBiso mean: 99.53 Å2
Baniso -1Baniso -2Baniso -3
1--9.9488 Å20 Å20 Å2
2---9.9488 Å20 Å2
3---19.8976 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å
Refinement stepCycle: 1 / Resolution: 2.45→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 85 100 2165
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012100HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12839HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d737SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes299HARMONIC5
X-RAY DIFFRACTIONt_it2100HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion16.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2432SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.56 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2237 140 4.89 %
Rwork0.2075 2721 -
all0.2082 2861 -
obs--99.97 %
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)
15.4962-1.90771.30093.11442.250211.4538-0.246-0.27480.94560.0236-0.020.0319-1.8725-1.15310.266-0.10550.50070.0303-0.4151-0.1552-0.3821248.885-26.0447239.367
20.9354-0.0684-0.32920.8729-0.06353.1124-0.0252-0.25930.09410.20740.0045-0.0308-0.46350.25490.0207-0.5853-0.0489-0.0236-0.5962-0.0308-0.5068278.969-43.2508233.937
32.2809-6.71610.69780.2142-1.93952.18250.1443-0.4675-0.36610.6258-0.0331-0.3575-0.1815-0.0551-0.11120.7606-0.0947-0.05050.4592-0.10420.462272.579-46.0907276.946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|-1 - A|108 }
2X-RAY DIFFRACTION2{ A|109 - A|234 }
3X-RAY DIFFRACTION3{ A|235 - A|261 }

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