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- PDB-4p9o: Complex of Voltage-gated ion channel in a the presence of channel... -

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Basic information

Entry
Database: PDB / ID: 4p9o
TitleComplex of Voltage-gated ion channel in a the presence of channel blocking compound
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / ion channel / membrane protein / channel blocker
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: 2.89 Å
AuthorsNaylor, C.E. / Bagneris, C. / Wallace, B.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H02070X 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 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 2.0Sep 20, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / diffrn_source / entity / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _atom_site.id / _citation.journal_id_CSD ..._atom_site.id / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_number_of_molecules / _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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 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

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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)69,94314
Polymers67,3464
Non-polymers2,59710
Water4,558253
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)70,70216
Polymers67,3464
Non-polymers3,35612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7320 Å2
ΔGint-54 kcal/mol
Surface area16700 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)69,18412
Polymers67,3464
Non-polymers1,8388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7030 Å2
ΔGint-49 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.420, 328.370, 80.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Ion transport protein


Mass: 16836.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus sp. (bacteria) / Strain: MC-1 / Gene: Mmc1_0798 / Plasmid: Pet15B / Production host: Escherichia coli (E. coli) / Strain (production host): C-41 / References: UniProt: A0L5S6
#2: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE BROMINE ION IS PART OF THE MOLECULE 2-(4-BROMOPHENYL)-1-(5-(4-CHLOROPHENYL)-1H-IMIDAZOL-2-YL) ...THE BROMINE ION IS PART OF THE MOLECULE 2-(4-BROMOPHENYL)-1-(5-(4-CHLOROPHENYL)-1H-IMIDAZOL-2-YL)ETHANAMINE, THE REST OF WHICH CAN NOT BE SEEN IN THE 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: 3.94 Å3/Da / Density % sol: 68.78 % / 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, 34% PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2013
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.89→45.24 Å / Num. obs: 24368 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 12.7
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.714 / Net I/σ(I) obs: 3.6 / % possible all: 99

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.89→32.91 Å / Cor.coef. Fo:Fc: 0.8963 / Cor.coef. Fo:Fc free: 0.8584 / SU R Cruickshank DPI: 0.344 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.353 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.265
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1251 5.19 %RANDOM
Rwork0.2139 ---
obs0.2158 24118 98.82 %-
Displacement parametersBiso mean: 61.82 Å2
Baniso -1Baniso -2Baniso -3
1-12.237 Å20 Å20 Å2
2---22.6386 Å20 Å2
3---10.4016 Å2
Refine analyzeLuzzati coordinate error obs: 0.393 Å
Refinement stepCycle: 1 / Resolution: 2.89→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 123 253 3232
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013234HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084566HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1001SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it3234HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion19.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
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_contact4027SEMIHARMONIC4
LS refinement shellResolution: 2.89→3.02 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2372 148 5.12 %
Rwork0.2075 2743 -
all0.209 2891 -
obs--98.82 %
Refinement TLS params.

T11: -0.304 Å2 / T22: 0.304 Å2 / T33: -0.304 Å2 / 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 °)T12 (Å2)T13 (Å2)T23 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6828-0.00830.25991.8824-1.3962.6325-0.04650.26060.54420.16410.1060.0349-0.54420.022-0.0595-0.0320.01750.0435-27.1291-62.795312.3211
23.94841.8585-0.80590.9379-0.71374.91820.0063-0.03880.493-0.01240.13580.2017-0.47620.2983-0.1421-0.0319-0.0105-0.0386-32.5063-63.050733.3795
35.24310.632-0.04811.2747-0.0882.1114-0.0285-0.023-0.5442-0.06850.1474-0.04380.37680.0472-0.11890.0117-0.05170.0166-28.6832-98.621430.0092
42.6129-1.35070.68741.969-0.07074.7957-0.02810.0973-0.43630.00890.12640.08670.5280.0635-0.09830.00730.0271-0.002-30.4638-98.48278.5121
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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