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- PDB-6sxf: Crystal Structure of the Voltage-Gated Sodium Channel NavMs (F208... -

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Basic information

Entry
Database: PDB / ID: 6sxf
TitleCrystal Structure of the Voltage-Gated Sodium Channel NavMs (F208L) in complex with Tamoxifen (2.8 Angstrom resolution)
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-CTX / Ion transport protein
Function and homology information
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.839 Å
AuthorsSula, A. / 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: Mol.Cell / Year: 2021
Title: A tamoxifen receptor within a voltage-gated sodium channel.
Authors: Sula, A. / Hollingworth, D. / Ng, L.C.T. / Larmore, M. / DeCaen, P.G. / Wallace, B.A.
History
DepositionSep 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,23517
Polymers62,3712
Non-polymers3,86415
Water2,432135
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)131,72732
Polymers124,7434
Non-polymers6,98428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area26550 Å2
ΔGint-244 kcal/mol
Surface area49760 Å2
MethodPISA
2
B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,21336
Polymers124,7434
Non-polymers8,47032
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area31340 Å2
ΔGint-264 kcal/mol
Surface area47640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.956, 107.956, 212.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-302-

NA

31A-303-

NA

41B-301-

NA

51B-302-

NA

61B-303-

NA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ion transport protein / Ion transporter


Mass: 31185.730 Da / Num. of mol.: 2
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, 150 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Chemical ChemComp-CTX / (Z)-2-[4-(1,2)-DIPHENYL-1-BUTENYL)-PHENOXY]-N,N-DIMETHYLETHANAMINE / TRANS FORM OF TAMOXIFEN / Tamoxifen


Mass: 371.515 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H29NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 5.19 Å3/Da / Density % sol: 76.32 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.839→76.34 Å / Num. obs: 30492 / % possible obs: 100 % / Redundancy: 15.4 % / CC1/2: 0.98 / Net I/σ(I): 6.3
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2195 / CC1/2: 0.865 / % possible all: 100

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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: 2.839→76.34 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.811 / SU R Cruickshank DPI: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.388 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 1495 4.91 %RANDOM
Rwork0.2198 ---
obs0.2222 30439 99.8 %-
Displacement parametersBiso max: 179.06 Å2 / Biso mean: 97.2 Å2 / Biso min: 40.31 Å2
Baniso -1Baniso -2Baniso -3
1--15.1968 Å20 Å20 Å2
2---15.1968 Å20 Å2
3---30.3936 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.839→76.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 221 135 4539
Biso mean--112.79 80.26 -
Num. residues----526
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1602SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes800HARMONIC5
X-RAY DIFFRACTIONt_it4467HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion589SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3866SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4496HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6088HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion19.78
LS refinement shellResolution: 2.84→2.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3401 30 4.93 %
Rwork0.2431 579 -
all0.2483 609 -
obs--97.44 %
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)
11.0367-0.01870.47790.5112-0.32843.98780.0116-0.3011-0.22250.31220.0158-0.05021.01010.1859-0.02740.11910.0742-0.0392-0.23010.0846-0.11664.321536.803685.477
20.9881-0.12510.3660.5490.06984.72550.0530.2894-0.2399-0.31930.01170.10851.1707-0.6355-0.06470.0898-0.1984-0.0554-0.1821-0.0848-0.1209-8.127438.325220.6731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 269
2X-RAY DIFFRACTION2{ B|* }B-1 - 269

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