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- PDB-4p30: Structure of NavMS mutant in presence of PI1 compound -

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Basic information

Entry
Database: PDB / ID: 4p30
TitleStructure of NavMS mutant in presence of PI1 compound
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / mutant / sodium channel / pore / 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 sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsBagneris, C. / Naylor, C.E. / 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
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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)70,69515
Polymers66,9224
Non-polymers3,77411
Water45025
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)70,67214
Polymers66,9224
Non-polymers3,75110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8840 Å2
ΔGint-98 kcal/mol
Surface area16680 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)70,71816
Polymers66,9224
Non-polymers3,79712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8500 Å2
ΔGint-136 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.260, 334.260, 80.040
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-304-

NA

21C-304-

NA

31D-302-

NA

DetailsAs confirmed by gel filtration, the asymmetric unit contains 2 independent half tetramers each of which are completed by crystallography symmetry.

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Components

#1: Protein
Ion transport protein


Mass: 16730.379 Da / Num. of mol.: 4 / Mutation: T207A, F214A
Source method: isolated from a genetically manipulated source
Details: pore and C-terminal domain only First 4 residues are from expression tag mutation at T207A and F214A to prevent compound binding
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


Mass: 546.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 4.01 Å3/Da / Density % sol: 69.33 % / Description: flat rectangular plate
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl, pH8, 34% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91407 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91407 Å / Relative weight: 1
ReflectionResolution: 3.31→45.73 Å / Num. obs: 16323 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 125.64 Å2 / Rmerge(I) obs: 0.148 / Net I/av σ(I): 4.1 / Net I/σ(I): 7.3
Reflection shellResolution: 3.31→3.57 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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Processing

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

3zjz


Resolution: 3.31→45.73 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.9082 / SU R Cruickshank DPI: 0.578 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.55 / SU Rfree Blow DPI: 0.314 / SU Rfree Cruickshank DPI: 0.319
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 823 5.05 %RANDOM
Rwork0.2036 ---
obs0.2047 16309 98.41 %-
Displacement parametersBiso mean: 75.07 Å2
Baniso -1Baniso -2Baniso -3
1-10.3537 Å20 Å20 Å2
2---19.566 Å20 Å2
3---9.2123 Å2
Refine analyzeLuzzati coordinate error obs: 0.639 Å
Refinement stepCycle: last / Resolution: 3.31→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 126 25 2990
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013107HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14290HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d983SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it3107HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion19.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion403SEMIHARMONIC5
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_contact3898SEMIHARMONIC4
LS refinement shellResolution: 3.31→3.54 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2675 138 4.81 %
Rwork0.2412 2729 -
all0.2425 2867 -
obs--98.41 %
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)
14.99590.95550.66362.0210.32012.67550.0378-0.00250.52970.0883-0.0230.4225-0.23460.1981-0.0148-0.2223-0.04630.05030.26180.0183-0.2133-27.6179-64.000111.132
23.2387-0.4855-0.68722.15381.0563.72040.08220.02090.4019-0.21380.02320.1084-0.53490.2189-0.1055-0.1116-0.039-0.03430.2638-0.0114-0.304-31.27-63.951532.4113
35.4706-0.057-0.23353.84750.69272.9084-0.06980.1203-0.54420.0615-0.1030.29940.42250.19130.1728-0.21840.0402-0.0130.2714-0.0116-0.2907-28.7527-99.80330.6361
44.22060.65440.04564.32510.0974.48050.03640.0417-0.51140.202-0.08150.03080.39270.21750.0451-0.16890.01710.05140.2814-0.0324-0.304-29.5489-99.76358.6873
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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