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- PDB-4pa6: Structure of NavMS pore and C-terminal domain crystallised in the... -

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Basic information

Entry
Database: PDB / ID: 4pa6
TitleStructure of NavMS pore and C-terminal domain crystallised in the presence of channel blocking compound
ComponentsIon transport proteinIon transporter
KeywordsTRANSPORT PROTEIN / channel blocking compound / sodium channel / pore / membrane protein
Function / homology
Function and homology information


monoatomic cation channel activity / plasma membrane
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å
AuthorsNaylor, C.E. / Bagneris, C. / Wallace, B.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H01070X United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J020702 United Kingdom
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism.
Authors: Bagneris, C. / DeCaen, P.G. / Naylor, C.E. / Pryde, D.C. / Nobeli, I. / Clapham, D.E. / Wallace, B.A.
#1: Journal: Nat Commun / Year: 2013
Title: Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
Authors: Bagneris, C. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W. / Wallace, B.A.
#2: Journal: Nat Commun / Year: 2012
Title: Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
Authors: McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,50313
Polymers67,3464
Non-polymers2,1579
Water25214
1
A: Ion transport protein
B: Ion transport protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)70,04914
Polymers67,3464
Non-polymers2,70310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7720 Å2
ΔGint-83 kcal/mol
Surface area16720 Å2
MethodPISA
2
C: Ion transport protein
D: Ion transport protein
hetero molecules

C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,95612
Polymers67,3464
Non-polymers1,6108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7390 Å2
ΔGint-120 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.934, 324.571, 79.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

NA

21B-302-

NA

31C-302-

NA

41C-303-

NA

51B-402-

HOH

61D-401-

HOH

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Components

#1: Protein
Ion transport protein / Ion transporter


Mass: 16836.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Pore and C-terminal domain / Source: (gene. exp.) Magnetococcus sp. (bacteria) / Strain: MC-1 / Gene: Mmc1_0798 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: A0L5S6
#2: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#3: 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
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CHANNEL PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF CHANNEL BLOCKING COMPOUND 4-BROMO- ...THE CHANNEL PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF CHANNEL BLOCKING COMPOUND 4-BROMO-LAMOTRIGINE BUT NO EVIDENCE FOR IT COULD BE IDENTIFIED IN THE ELECTRON DENSITY MAPS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.98 % / Description: Flat rectangular plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Sodium ctirate, 0.1 M TRIS, pH 8.0, 34 % PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2013
RadiationMonochromator: channel cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 3.36→44.77 Å / Num. obs: 15259 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 99.63 Å2 / Rmerge(I) obs: 0.184 / Net I/σ(I): 12
Reflection shellResolution: 3.36→3.63 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 4.4 / % possible all: 98.9

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: using 3ZJZ as starting model

3zjz


Resolution: 3.36→44.77 Å / Cor.coef. Fo:Fc: 0.8419 / Cor.coef. Fo:Fc free: 0.7534 / SU R Cruickshank DPI: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.914 / SU Rfree Blow DPI: 0.495 / SU Rfree Cruickshank DPI: 0.504
RfactorNum. reflection% reflectionSelection details
Rfree0.3421 792 5.2 %RANDOM
Rwork0.3019 ---
obs0.3041 15245 99.66 %-
Displacement parametersBiso mean: 72.75 Å2
Baniso -1Baniso -2Baniso -3
1-12.572 Å20 Å20 Å2
2---21.2882 Å20 Å2
3---8.7162 Å2
Refine analyzeLuzzati coordinate error obs: 0.963 Å
Refinement stepCycle: 1 / Resolution: 3.36→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 80 14 2950
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013015HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14114HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d945SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it3015HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion22.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3895SEMIHARMONIC4
LS refinement shellResolution: 3.36→3.59 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2576 135 5.09 %
Rwork0.2171 2519 -
all0.2192 2654 -
obs--99.66 %
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)
14.07151.6543-1.36482.11111.38814.5671-0.0178-0.0824-0.26710.0460.1963-0.22520.22860.0325-0.1785-0.41980.0441-0.04580.608-0.0829-0.445-11.0815-97.6827-30.0535
26.71751.4161.91541.2947-0.96695.5654-0.1120.1264-0.2627-0.15670.201-0.07880.2213-0.0081-0.0889-0.4424-0.060.03560.608-0.0195-0.5235-10.137-97.444-8.7189
35.6544-1.77732.11871.9370.14964.4679-0.04330.23920.5082-0.16960.3262-0.511-0.4046-0.165-0.2829-0.4314-0.02550.10440.6069-0.1361-0.3665-12.6127-61.7973-11.7633
45.5884-1.4578-2.75991.3874-2.19864.6085-0.1114-0.05550.38440.30630.3084-0.2705-0.5797-0.0644-0.197-0.31530.1053-0.06860.608-0.0166-0.4966-8.2489-61.87-32.3392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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