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

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Basic information

Entry
Database: PDB / ID: 6sxe
TitleCrystal Structure of the Voltage-Gated Sodium Channel NavMs (F208L) in complex with Endoxifen (2.6 Angstrom resolution)
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Voltage Gated Sodium Channel / Membrane protein
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 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / Endoxifen / Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSula, A. / Hollingworth, D. / Wallace, B.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/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

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1459
Polymers31,1861
Non-polymers1,9598
Water90150
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)132,58036
Polymers124,7434
Non-polymers7,83832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area23120 Å2
ΔGint-215 kcal/mol
Surface area51710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.108, 110.108, 210.164
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


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, 58 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.: 2 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#4: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O9
#5: Chemical ChemComp-9XY / Endoxifen / 4-[(1Z)-1-{4-[2-(methylamino)ethoxy]phenyl}-2-phenylbut-1-en-1-yl]phenol


Mass: 373.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 5.22 Å3/Da / Density % sol: 76.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M MgCl2 hexahydrate, 0.1 M HEPES buffer, pH 8, 30% v/v polyethylene glycol (PEG) 500 and 4% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.97966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97966 Å / Relative weight: 1
ReflectionResolution: 2.6→52.54 Å / Num. obs: 20152 / % possible obs: 99.1 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2435 / CC1/2: 0.826 / % possible all: 100

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Processing

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

5hvx


Resolution: 2.6→52.54 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.87 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.278 939 4.66 %RANDOM
Rwork0.238 ---
obs0.24 20151 99.1 %-
Displacement parametersBiso max: 276.3 Å2 / Biso mean: 108.44 Å2 / Biso min: 45.82 Å2
Baniso -1Baniso -2Baniso -3
1--12.5915 Å20 Å20 Å2
2---12.5915 Å20 Å2
3---25.183 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.6→52.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 114 50 2309
Biso mean--142.45 95.03 -
Num. residues----271
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d829SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes416HARMONIC5
X-RAY DIFFRACTIONt_it2305HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion301SEMIHARMONIC5
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_contact2721SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2305HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3107HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion20.23
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 46
RfactorNum. reflection% reflection
Rfree0.1975 20 4.56 %
Rwork0.2112 419 -
all0.2104 439 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.2493 Å / Origin y: 6.0926 Å / Origin z: 32.0674 Å
111213212223313233
T-0.3479 Å2-0.0771 Å2-0.1087 Å2--0.2518 Å2-0.009 Å2---0.4198 Å2
L0.5145 °2-0.0893 °20.3224 °2-1.219 °20.2929 °2--2.3405 °2
S-0.0833 Å °-0.1643 Å °0.074 Å °0.2883 Å °0.0202 Å °-0.2849 Å °-0.2841 Å °0.6257 Å °0.0631 Å °
Refinement TLS groupSelection details: { A|* }

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