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- PDB-5bzb: NavMs voltage-gated sodium channel pore and C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5bzb
TitleNavMs voltage-gated sodium channel pore and C-terminal domain
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / SELECTIVITY FILTER / MEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
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 marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNaylor, C.E. / Bagneris, C. / Wallace, B.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H01070X United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J020702 United Kingdom
Citation
Journal: Embo J. / Year: 2016
Title: Molecular basis of ion permeability in a voltage-gated sodium channel.
Authors: Naylor, C.E. / Bagneris, C. / DeCaen, P.G. / Sula, A. / Scaglione, A. / 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
DepositionJun 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)70,64217
Polymers67,3464
Non-polymers3,29613
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-85 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.340, 332.763, 80.380
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-302-

NA

21A-303-

NA

31A-304-

NA

41C-302-

NA

51C-303-

NA

61D-303-

NA

71A-443-

HOH

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Components

#1: Protein
Ion transport protein / navms


Mass: 16836.502 Da / Num. of mol.: 4
Fragment: navms pore and c-terminal domain, UNP residues 130-274
Source method: isolated from a genetically manipulated source
Details: c-terminal is not visible in the electron density / Source: (gene. exp.) Magnetococcus marinus MC-1 (bacteria) / Gene: Mmc1_0798 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0L5S6
#2: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 379.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 7.58 Å3/Da / Density % sol: 83.77 % / Description: flat plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1m na3citrate, 0.1m tris ph 8.0, 34% peg 400 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2013
RadiationMonochromator: si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 2.7→57.81 Å / Num. all: 30179 / Num. obs: 30149 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 40.38 Å2 / Rmerge(I) obs: 0.245 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimless0.1.29data scaling
BUSTER2.10.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZJZ

3zjz


Resolution: 2.7→57.81 Å / Cor.coef. Fo:Fc: 0.9003 / Cor.coef. Fo:Fc free: 0.8265 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1548 5.14 %RANDOM
Rwork0.1783 ---
obs0.1801 30134 99.78 %-
Displacement parametersBiso mean: 46.51 Å2
Baniso -1Baniso -2Baniso -3
1-2.1882 Å20 Å20 Å2
2---5.9798 Å20 Å2
3---3.7916 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: 1 / Resolution: 2.7→57.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 158 255 3269
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013089HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014198HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1007SINUSOIDAL2
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_it3089HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion17.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
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
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2241 145 5 %
Rwork0.1844 2756 -
all0.1864 2901 -
obs--99.97 %
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)
13.2148-0.199-0.40251.07360.22482.89680.06250.08670.4879-0.0505-0.05170.0702-0.47880.0445-0.0108-0.2749-0.03810.00770.24640.0179-0.2306-27.7612-63.598511.765
23.6104-0.40550.91781.15410.27473.2808-0.0386-0.04630.4639-0.0603-0.0582-0.0551-0.46890.18010.0968-0.2507-0.01850.00530.2756-0.0263-0.2958-31.963-63.849832.5307
33.7979-0.12080.59911.6805-0.10983.05530.0725-0.1243-0.40240.0654-0.05310.00930.3917-0.0595-0.0193-0.28860.0177-0.01370.25720.0051-0.2754-28.8204-99.51230.2026
43.622-0.3224-0.23161.4460.22343.2855-0.0268-0.1337-0.3552-0.0070.0122-0.07010.3950.07180.0146-0.2620.01680.01510.2615-0.0137-0.2953-30.2001-99.45239.0952
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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