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- PDB-6yz0: Full length Open-form Sodium Channel NavMs F208L in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6yz0
TitleFull length Open-form Sodium Channel NavMs F208L in complex with Cannabidiol (CBD)
ComponentsIon transport proteinIon transporter
KeywordsMETAL TRANSPORT / Voltage Gated Sodium Channel / Membrane protein.
Function / homologyVoltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / plasma membrane / Chem-CD0 / Ion transport protein
Function and homology information
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSula, A. / Sait, L.G. / Hollingworth, D. / Wallace, B.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L006790, BB/N012763 and BB/R001294 United Kingdom
CitationJournal: Elife / Year: 2020
Title: Cannabidiol interactions with voltage-gated sodium channels.
Authors: Sait, L.G. / Sula, A. / Ghovanloo, M.R. / Hollingworth, D. / Ruben, P.C. / Wallace, B.A.
History
DepositionMay 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)32,4977
Polymers31,1861
Non-polymers1,3126
Water1,18966
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)129,98928
Polymers124,7434
Non-polymers5,24624
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 area19960 Å2
ΔGint-183 kcal/mol
Surface area50460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.328, 110.328, 207.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Ion transporter


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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L5S6

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Non-polymers , 5 types, 72 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 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Chemical ChemComp-CD0 / 2-[(1R,2R,5S)-5-methyl-2-(prop-1-en-2-yl)cyclohexyl]-5-pentylbenzene-1,3-diol


Mass: 316.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H32O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 74.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M lithium sulphate, 0.1M HEPES, pH 7, and 40% v/v PEG200.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.3→103.94 Å / Num. obs: 29849 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2770 / CC1/2: 0.877

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVX

5hvx


Resolution: 2.3→103.94 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.163
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1452 5.06 %RANDOM
Rwork0.2472 ---
obs0.2479 28706 99.2 %-
Displacement parametersBiso max: 233.55 Å2 / Biso mean: 110.79 Å2 / Biso min: 50.76 Å2
Baniso -1Baniso -2Baniso -3
1--21.6961 Å20 Å20 Å2
2---21.6961 Å20 Å2
3---43.3922 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.3→103.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 57 66 2122
Biso mean--106.11 101.87 -
Num. residues----257
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d726SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it2099HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion285SEMIHARMONIC5
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_contact1836SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2099HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2847HARMONIC20.86
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion16.32
LS refinement shellResolution: 2.3→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2544 29 5.04 %
Rwork0.25 546 -
all0.2503 575 -
obs--99.82 %
Refinement TLS params.Method: refined / Origin x: 48.1058 Å / Origin y: 72.7555 Å / Origin z: 30.8819 Å
111213212223313233
T0.087 Å20.0067 Å2-0.0106 Å2--0.2273 Å2-0.0987 Å2---0.0024 Å2
L2.5883 °2-0.8813 °2-1.3234 °2-0.678 °20.6776 °2--2.4392 °2
S-0.0837 Å °-0.2998 Å °0.0078 Å °0.3032 Å °-0.0617 Å °-0.0575 Å °-0.5442 Å °0.0865 Å °0.1455 Å °
Refinement TLS groupSelection details: { A|* }

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