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- PDB-6z8c: Crystal Structure of the Voltage-Gated Sodium Channel NavMs (F208... -

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Basic information

Entry
Database: PDB / ID: 6z8c
TitleCrystal Structure of the Voltage-Gated Sodium Channel NavMs (F208L) in complex with N-desmethyltamoxifen (3.2 A 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
Chem-QBN / Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
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)33,2759
Polymers31,1861
Non-polymers2,0908
Water72140
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)133,10136
Polymers124,7434
Non-polymers8,35832
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 area24940 Å2
ΔGint-240 kcal/mol
Surface area52660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.221, 109.221, 211.161
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 / Mutation: F208L
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, 48 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-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-QBN / 2-[4-[(~{Z})-1,2-diphenylbut-1-enyl]phenoxy]-~{N}-methyl-ethanamine


Mass: 357.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 5.05 Å3/Da / Density % sol: 75.64 % / Description: Bipyramids
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08 M Sodium chloride; 0.1 M MES pH 6.5; 37 % v/v PEG 400; 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: 0.96864 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 3.2→48.51 Å / Num. obs: 10937 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.99 / Net I/σ(I): 6.6
Reflection shellResolution: 3.2→3.42 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1934 / CC1/2: 0.81

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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: 3.2→48.51 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.007 / SU Rfree Blow DPI: 0.388 / SU Rfree Cruickshank DPI: 0.389
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 577 5.28 %RANDOM
Rwork0.2535 ---
obs0.2541 10934 100 %-
Displacement parametersBiso max: 170.47 Å2 / Biso mean: 85.86 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--7.6025 Å20 Å20 Å2
2---7.6025 Å20 Å2
3---15.2049 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 3.2→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 107 40 2292
Biso mean--105.47 65.62 -
Num. residues----271
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d818SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes372HARMONIC5
X-RAY DIFFRACTIONt_it2292HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion302SEMIHARMONIC5
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_contact1947SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2292HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3092HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion21.69
LS refinement shellResolution: 3.2→3.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.307 16 4.09 %
Rwork0.2328 375 -
all0.2352 391 -
obs--99.75 %
Refinement TLS params.Method: refined / Origin x: 17.2622 Å / Origin y: 6.0845 Å / Origin z: 32.1706 Å
111213212223313233
T0.0176 Å2-0.0768 Å2-0.0557 Å2-0.1553 Å2-0.0003 Å2---0.0895 Å2
L0.0657 °2-0.0001 °20.043 °2-0.4497 °20.019 °2--1.4877 °2
S-0.018 Å °-0.0673 Å °-0.0725 Å °0.0623 Å °-0.0062 Å °-0.1269 Å °-0.1494 Å °0.5279 Å °0.0241 Å °
Refinement TLS groupSelection details: { A|* }

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