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- PDB-4x89: NavMs voltage-gated sodium channal pore and C-terminal domain soa... -

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Basic information

Entry
Database: PDB / ID: 4x89
TitleNavMs voltage-gated sodium channal pore and C-terminal domain soaked with Silver nitrate
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
SILVER ION / Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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
DepositionDec 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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)70,08620
Polymers67,3464
Non-polymers2,74016
Water4,810267
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)70,00120
Polymers67,3464
Non-polymers2,65516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area9500 Å2
ΔGint-129 kcal/mol
Surface area15980 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)70,17120
Polymers67,3464
Non-polymers2,82516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8950 Å2
ΔGint-97 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.000, 329.240, 80.020
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

21A-304-

NA

31A-305-

NA

41A-306-

NA

51C-303-

NA

61C-304-

NA

71D-303-

NA

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ion transport protein


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
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

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Non-polymers , 5 types, 283 molecules

#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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 7.43 Å3/Da / Density % sol: 83.5 % / Description: Flat plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.77 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.62→45.31 Å / Num. all: 32401 / Num. obs: 32142 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 52.94 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 7.5
Reflection shellResolution: 2.62→2.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.7 / % possible all: 94.9

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZJZ

3zjz


Resolution: 2.62→45.25 Å / Cor.coef. Fo:Fc: 0.8794 / Cor.coef. Fo:Fc free: 0.8885 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 1635 5.11 %RANDOM
Rwork0.228 ---
obs0.2289 31990 98.77 %-
Displacement parametersBiso mean: 45.97 Å2
Baniso -1Baniso -2Baniso -3
1-9.4686 Å20 Å20 Å2
2---16.8933 Å20 Å2
3---7.4248 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: 1 / Resolution: 2.62→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 131 267 3254
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013059HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034156HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d982SINUSOIDAL2
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_it3059HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion18.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance7HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3917SEMIHARMONIC4
LS refinement shellResolution: 2.62→2.71 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2918 138 5.03 %
Rwork0.2599 2608 -
all0.2615 2746 -
obs--98.77 %
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)
14.64540.48370.13221.1422-0.59514.40150.12150.21320.65150.0858-0.15550.1453-0.6410.11780.0339-0.0141-0.04410.02020.191-0.0014-0.03-27.7334-63.64611.7935
24.31890.2153-0.00121.12850.42634.48450.0634-0.14350.5473-0.07-0.0919-0.012-0.68580.33120.02850.04710.0005-0.00610.2021-0.0425-0.0908-31.3557-63.688332.2446
34.3917-0.15830.06880.659-0.11333.78120.0758-0.1546-0.6623-0.0071-0.13530.04440.63730.07430.05950.04150.0336-0.01970.26060.0030.0151-28.7971-99.495530.1699
44.1758-0.4096-0.41790.79240.35223.523-0.0071-0.0363-0.54950.0627-0.02360.02670.6570.24130.03060.02350.00850.0080.1582-0.0108-0.0869-29.593-99.67729.2357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|131 - B|220 }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|130 - D|220 }

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