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- PDB-4pa4: Structure of NavMS in complex with channel blocking compound -

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Basic information

Entry
Database: PDB / ID: 4pa4
TitleStructure of NavMS in complex with channel blocking compound
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / channel blocking compound / 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
BROMIDE ION / Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.02 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 / 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_related / pdbx_database_status / pdbx_struct_assembly / 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.country / _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 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 0 : statistics at the very beginning when nothing is done yet

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)70,27819
Polymers67,3464
Non-polymers2,93215
Water23413
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)71,39422
Polymers67,3464
Non-polymers4,04818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area11400 Å2
ΔGint-242 kcal/mol
Surface area15550 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)69,16216
Polymers67,3464
Non-polymers1,81612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8150 Å2
ΔGint-149 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.890, 327.330, 79.940
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-305-

NA

21A-306-

NA

31D-401-

NA

41D-403-

NA

51A-402-

HOH

61C-404-

HOH

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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
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

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Non-polymers , 5 types, 28 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-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE BROMINE ION IS PART OF THE COMPOUND AMINO-6-BROMOBENZOTHIAZOLE, THE REST OF WHICH IS NOT ...THE BROMINE ION IS PART OF THE COMPOUND AMINO-6-BROMOBENZOTHIAZOLE, THE REST OF WHICH IS NOT VISIBLE IN THE ELECTRON DENSITY DUE TO LOW OCCUPANCY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.3 % / Description: Flat REctangular plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M sodium citrate, 0.1 M Tris, pH 8.0, 34 % PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91963 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91963 Å / Relative weight: 1
ReflectionResolution: 3.02→45.06 Å / Num. obs: 21190 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 70.87 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.8
Reflection shellResolution: 3.02→3.2 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.1 / % possible all: 98

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 3.02→45.06 Å / Cor.coef. Fo:Fc: 0.8966 / Cor.coef. Fo:Fc free: 0.9255 / SU R Cruickshank DPI: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.388 / SU Rfree Blow DPI: 0.272 / SU Rfree Cruickshank DPI: 0.277
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1095 5.18 %RANDOM
Rwork0.2303 ---
obs0.231 21127 99.91 %-
Displacement parametersBiso mean: 91.26 Å2
Baniso -1Baniso -2Baniso -3
1-6.8267 Å20 Å20 Å2
2---8.2766 Å20 Å2
3---1.4499 Å2
Refine analyzeLuzzati coordinate error obs: 0.675 Å
Refinement stepCycle: 1 / Resolution: 3.02→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 105 13 3011
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013070HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094176HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d981SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes446HARMONIC5
X-RAY DIFFRACTIONt_it3070HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.37
X-RAY DIFFRACTIONt_other_torsion19.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion408SEMIHARMONIC5
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_contact3866SEMIHARMONIC4
LS refinement shellResolution: 3.02→3.17 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2497 137 4.98 %
Rwork0.2238 2615 -
all0.2253 2752 -
obs--99.91 %
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)
15.37430.51631.13411.3697-0.93233.8049-0.18170.08740.78420.10920.37870.1675-0.46940.0405-0.197-0.4164-0.03370.03231.26520.1054-0.4106-28.684-63.449711.0104
23.94010.8088-1.35890.1140.20746.3621-0.1337-0.05380.4301-0.01030.27890.1499-0.80640.0475-0.1452-0.3951-0.1214-0.03471.2164-0.0347-0.493-31.0277-63.411231.5351
36.4080.2239-0.60711.4707-0.08343.842-0.1406-0.1809-0.90440.190.3221-0.00740.69360.0216-0.1814-0.48360.0093-0.0661.22030.0877-0.5141-29.6867-99.683430.8193
44.5663-0.44490.96591.4016-0.62116.9453-0.0603-0.1179-0.7326-0.05730.2293-0.060.95640.1425-0.169-0.4350.0860.04421.20540.0035-0.5272-29.3104-99.66119.6418
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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