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- PDB-4pa7: Structure of NavMS pore and C-terminal domain crystallised in pre... -

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Basic information

Entry
Database: PDB / ID: 4pa7
TitleStructure of NavMS pore and C-terminal domain crystallised in presence of 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
Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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_detector ...citation / diffrn_detector / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.pdbx_collection_date ..._citation.journal_id_CSD / _diffrn_detector.pdbx_collection_date / _diffrn_source.pdbx_synchrotron_site / _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_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 1.4Sep 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
Remark 0 : statistics at the very beginning when nothing is done yet

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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)70,66518
Polymers67,3464
Non-polymers3,31914
Water50428
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)71,23420
Polymers67,3464
Non-polymers3,88816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area11340 Å2
ΔGint-230 kcal/mol
Surface area14850 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)70,09516
Polymers67,3464
Non-polymers2,74912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area9000 Å2
ΔGint-136 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.810, 328.860, 79.920
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
11B-304-

NA

21D-303-

NA

31A-402-

HOH

41B-406-

HOH

51D-408-

HOH

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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
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
#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.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CHANNEL PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF THE CHANNEL-BLOCKING COMPOUND 4- ...THE CHANNEL PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF THE CHANNEL-BLOCKING COMPOUND 4-BROMOBENZYLAMINE, BUT NO EVIDENCE FOR IT COULD BE SEEN IN THE ELECTRON DENSITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.41 % / 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: 0.91966 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2003
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91966 Å / Relative weight: 1
ReflectionResolution: 3.02→45.2 Å / Num. obs: 21117 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 64.32 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 9.7
Reflection shellResolution: 3.02→3.21 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.4 / % possible all: 99

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: using 3ZJZ as a starting molecule

3zjz


Resolution: 3.02→45.2 Å / Cor.coef. Fo:Fc: 0.8828 / Cor.coef. Fo:Fc free: 0.9048 / SU R Cruickshank DPI: 0.437 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.427 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.301
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1093 5.18 %RANDOM
Rwork0.2512 ---
obs0.2519 21096 99.47 %-
Displacement parametersBiso mean: 73.78 Å2
Baniso -1Baniso -2Baniso -3
1-10.0495 Å20 Å20 Å2
2---16.6475 Å20 Å2
3---6.598 Å2
Refine analyzeLuzzati coordinate error obs: 0.715 Å
Refinement stepCycle: 1 / Resolution: 3.02→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 135 28 3012
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013057HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14151HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d989SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes439HARMONIC5
X-RAY DIFFRACTIONt_it3057HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion19.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
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_contact3845SEMIHARMONIC4
LS refinement shellResolution: 3.02→3.17 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2388 132 4.95 %
Rwork0.2274 2533 -
all0.2281 2665 -
obs--99.47 %
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)
16.0928-0.01111.0840.9083-0.09444.5945-0.07560.04120.65310.08390.23850.0418-0.6295-0.0049-0.163-0.2322-0.00770.03790.93780.0801-0.2405-27.7334-63.64611.7935
25.82210.4582-1.77451.4469-0.01547.0696-0.07430.03790.5977-0.09210.24670.1209-0.74430.0855-0.1724-0.2258-0.0766-0.03360.937-0.0306-0.3004-31.3557-63.688332.2446
35.8216-0.6026-1.33862.7818-0.35735.3144-0.1015-0.0516-0.57420.0630.19870.07820.7170.0319-0.0972-0.2631-0.0249-0.06090.94850.0557-0.32-28.7971-99.495530.1699
45.59-0.48742.48322.94930.89886.10290.024-0.0539-0.67720.12410.21130.01930.6020.1303-0.2353-0.30880.07510.06130.87720.0273-0.3765-29.593-99.67729.2357
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|131 - D|220 }

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