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- PDB-5yuc: Crystal structure of voltage-gated sodium channel NavAb N49K mutant -

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Basic information

Entry
Database: PDB / ID: 5yuc
TitleCrystal structure of voltage-gated sodium channel NavAb N49K mutant
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.40099156989 Å
AuthorsIrie, K. / Shimomura, T. / Fujiyoshi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Toyoaki Scholarship Foundation Japan
CitationJournal: FEBS Lett. / Year: 2017
Title: Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb.
Authors: Irie, K. / Haga, Y. / Shimomura, T. / Fujiyoshi, Y.
History
DepositionNov 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5804
Polymers31,3971
Non-polymers1,1833
Water00
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,31916
Polymers125,5894
Non-polymers4,73012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area18860 Å2
ΔGint-194 kcal/mol
Surface area46470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.440, 127.440, 202.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1301-

CA

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Components

#1: Protein Ion transport protein / voltage gated sodium channel


Mass: 31397.279 Da / Num. of mol.: 1 / Mutation: N49K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Gene: SAMEA4475700_01771 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239WB15, UniProt: A8EVM5*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium


Mass: 631.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM

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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: 6.56 Å3/Da / Density % sol: 81.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 11% polyethylene glycol monomethyl ether 2000, 100 mM NaCl, 100 mM calcium nitrate, 100 mM Tris-HCl, pH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→41.18 Å / Num. obs: 11809 / % possible obs: 87.26 % / Redundancy: 13.6 % / Biso Wilson estimate: 26.8946442452 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.0708 / Net I/σ(I): 13.6
Reflection shellResolution: 3.4→3.523 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUA

5yua


Resolution: 3.40099156989→41.1749446498 Å / SU ML: 0.38991684011 / Cross valid method: FREE R-VALUE / σ(F): 1.36042076047 / Phase error: 29.6502317313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.278677630996 1035 9.98938326416 %
Rwork0.229802342198 9326 -
obs0.234673895642 10361 87.3903508772 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.8269332284 Å2
Refinement stepCycle: LAST / Resolution: 3.40099156989→41.1749446498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 66 0 1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112943454591986
X-RAY DIFFRACTIONf_angle_d1.173032512192705
X-RAY DIFFRACTIONf_chiral_restr0.0646484954044335
X-RAY DIFFRACTIONf_plane_restr0.0061289094648309
X-RAY DIFFRACTIONf_dihedral_angle_d6.054199623241143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.401-3.58020.356101450692520.246384717589483X-RAY DIFFRACTION32.3262839879
3.5802-3.80440.2842177432311340.2341646438421201X-RAY DIFFRACTION81.1550151976
3.8044-4.09790.2868481148831670.2228888184091500X-RAY DIFFRACTION99.4630071599
4.0979-4.50980.2483401649521670.2079805340621499X-RAY DIFFRACTION99.8202516477
4.5098-5.16130.2262179633491670.1877819287631510X-RAY DIFFRACTION99.7027348395
5.1613-6.49850.2949787729021710.2833317581371533X-RAY DIFFRACTION99.7074312463
6.4985-41.17790.3183487132011770.2537249188661600X-RAY DIFFRACTION98.0684326711
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)
11.45797198937-0.1536813072250.3029542882231.38060650309-0.9192090286380.6458482176160.1450727862240.261886944261-0.274370920392-0.0189236399273-0.14115966138-0.3663832045670.4627548875950.38067694139-0.03997790641370.705706299780.362841634657-0.1317596950340.9115155036240.1503038785550.62672451520732.048511805-23.258027712828.6042459003
21.08787056818-0.06889984139610.4047527747791.01865563911-0.01645479193511.45781154742-0.0896698605615-0.198434895123-0.1987237986350.247235935636-0.0486548824402-0.1205722181040.248833611050.1224443453280.1236269611420.2123646949-0.03961032395880.07592314963190.1970391281160.06992550711590.11927635159-1.3954654685-13.225014966423.4264760003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 999 through 1096 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1097 through 1227 )

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