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- PDB-8s6j: NavMs in complex with riluzole -

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Basic information

Entry
Database: PDB / ID: 8s6j
TitleNavMs in complex with riluzole
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / Voltage-Gated Sodium Channel
Function / homologyVoltage-gated cation channel calcium and sodium / voltage-gated sodium channel complex / voltage-gated sodium channel activity / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine / Chem-PG6 / Ion transport protein
Function and homology information
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHollingworth, D. / Sula, A. / Mykhaylyk, V. / Wallace, B.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BSB51 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for the rescue of hyperexcitable cells by the amyotrophic lateral sclerosis drug Riluzole.
Authors: Hollingworth, D. / Thomas, F. / Page, D.A. / Fouda, M.A. / De Castro, R.L. / Sula, A. / Mykhaylyk, V.B. / Kelly, G. / Ulmschneider, M.B. / Ruben, P.C. / Wallace, B.A.
History
DepositionFeb 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification

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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)32,2069
Polymers31,1861
Non-polymers1,0208
Water50428
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)128,82236
Polymers124,7434
Non-polymers4,08032
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 area22620 Å2
ΔGint-309 kcal/mol
Surface area50330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.17, 109.17, 208.925
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-302-

NA

31A-303-

NA

41A-409-

HOH

51A-415-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ion transport protein


Mass: 31185.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus MC-1 (bacteria) / Gene: Mmc1_0798 / Details (production host): pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0L5S6

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Non-polymers , 6 types, 36 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-657 / 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine / Riluzole


Mass: 234.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5F3N2OS / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 35%vPEG 300 100mM HEPES 100mM NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.755 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 2, 2020
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.755 Å / Relative weight: 1
ReflectionResolution: 2.15→96.944 Å / Num. obs: 34745 / % possible obs: 100 % / Redundancy: 16 % / Biso Wilson estimate: 43.8 Å2 / CC1/2: 0.979 / Net I/σ(I): 2.63
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 7.7 % / Num. unique obs: 2799 / CC1/2: 0.972 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→96.757 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.221 / SU B: 4.16 / SU ML: 0.104 / Average fsc free: 0.955 / Average fsc work: 0.9608 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.136 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2447 1749 5.035 %
Rwork0.229 32987 -
all0.23 --
obs-34736 99.997 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 67.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å2-0 Å20 Å2
2--0.061 Å2-0 Å2
3----0.122 Å2
Refinement stepCycle: LAST / Resolution: 2.15→96.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 64 28 2114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122135
X-RAY DIFFRACTIONr_angle_refined_deg2.1781.8092893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.272517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3910370
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.0461082
X-RAY DIFFRACTIONr_chiral_restr0.1460.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021529
X-RAY DIFFRACTIONr_nbd_refined0.2440.2925
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.214
X-RAY DIFFRACTIONr_mcbond_it8.0966.5471024
X-RAY DIFFRACTIONr_mcangle_it11.06611.6851278
X-RAY DIFFRACTIONr_scbond_it9.226.9921111
X-RAY DIFFRACTIONr_scangle_it12.59312.6481612
X-RAY DIFFRACTIONr_lrange_it14.68268.353251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.15-2.2060.3141420.32323930.32325350.9270.9170.264
2.206-2.2660.3071120.29423400.29524520.930.9350.255
2.266-2.3320.3031200.27622620.27723820.9350.9430.233
2.332-2.4040.2961330.26122150.26323480.9380.9520.227
2.404-2.4830.2571350.23421290.23522640.9560.9640.193
2.483-2.570.235980.22420710.22521690.9630.9680.18
2.57-2.6670.2541000.21820180.2221180.9630.9710.187
2.667-2.7750.227920.20719620.20820540.9670.9730.18
2.775-2.8990.251070.20418530.20719600.9650.9750.184
2.899-3.040.228980.21517700.21618680.9690.9710.197
3.04-3.2040.232810.21417170.21517980.9670.9710.201
3.204-3.3980.228790.22516170.22516960.9710.9680.214
3.398-3.6330.234760.21115320.21216080.9680.9750.206
3.633-3.9230.251920.21414110.21715030.9590.9730.216
3.923-4.2970.221720.21713130.21713850.9670.9730.221
4.297-4.8030.204460.19712240.19712700.9740.9790.208
4.803-5.5440.213590.20310480.20311070.970.9770.215
5.544-6.7840.253430.2449320.2449750.9620.9680.257
6.784-9.5710.205430.2177250.2167680.980.9760.242
9.571-96.7570.347210.3254550.3264760.8750.8970.352

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