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- PDB-5yua: Crystal structure of voltage-gated sodium channel NavAb in high-p... -

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Basic information

Entry
Database: PDB / ID: 5yua
TitleCrystal structure of voltage-gated sodium channel NavAb in high-pH condition
ComponentsIon transport proteinIon transporter
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


monoatomic cation channel activity / identical protein binding / plasma membrane
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
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8008556672 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

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,14911
Polymers31,3821
Non-polymers5,76710
Water1629
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)148,59644
Polymers125,5294
Non-polymers23,06740
Water724
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 area53040 Å2
ΔGint-245 kcal/mol
Surface area41750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.450, 126.450, 201.658
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

21A-1401-

HOH

31A-1402-

HOH

41A-1403-

HOH

51A-1405-

HOH

61A-1406-

HOH

71A-1408-

HOH

81A-1409-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

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


Mass: 31382.205 Da / Num. of mol.: 1
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
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 17 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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 / CHAPS detergent


Mass: 631.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM
#5: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 6.42 Å3/Da / Density % sol: 80.85 % / Description: pyramidal shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→31.47 Å / Num. obs: 20186 / % possible obs: 87.68 % / Redundancy: 9.1 % / Biso Wilson estimate: 60.9798776849 Å2 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.087 / Net I/σ(I): 14.02
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.3136 / Num. unique obs: 505 / Rpim(I) all: 1.074 / % possible all: 25.29

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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: 3RVY

3rvy


Resolution: 2.8008556672→31.4605001582 Å / SU ML: 0.447921114119 / Cross valid method: FREE R-VALUE / σ(F): 1.33590617468 / Phase error: 30.3553703658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.262134745718 921 5.12093411176 %
Rwork0.230018187795 17064 -
obs0.231669922293 17985 87.778808141 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.7405017713 Å2
Refinement stepCycle: LAST / Resolution: 2.8008556672→31.4605001582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 379 9 2248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009603630179142290
X-RAY DIFFRACTIONf_angle_d1.324927321173065
X-RAY DIFFRACTIONf_chiral_restr0.0575773173154356
X-RAY DIFFRACTIONf_plane_restr0.00660838643893321
X-RAY DIFFRACTIONf_dihedral_angle_d24.1358211822931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.94840.402671622931360.371466001008872X-RAY DIFFRACTION31.7815890795
2.9484-3.1330.4312320422311450.3671309716862484X-RAY DIFFRACTION91.3164293157
3.133-3.37460.3604236761861420.3138625075542734X-RAY DIFFRACTION99.8957971518
3.3746-3.71380.2691096336271510.2264845092132754X-RAY DIFFRACTION99.9655884377
3.7138-4.250.2202091587851580.1896443496752756X-RAY DIFFRACTION99.9656946827
4.25-5.35030.2075567245271670.1698801813742774X-RAY DIFFRACTION99.5262267343
5.3503-31.46250.2482916876811220.2349905032832690X-RAY DIFFRACTION90.826873385
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)
11.881544574250.164697662563-0.5661582966873.08004125224-1.679087574232.65343052530.1107103499210.139727543662-0.377643891910.00700365601287-0.176593802515-0.4027196538791.093280652251.206754973660.06346056098950.976148853760.455118235716-0.174467141111.225634122750.1432190295580.87156612048931.2436357695-23.449719336428.367579038
23.95836188923-0.3674688061111.086248026452.19757319368-0.3861800282263.48468935291-0.127771737926-0.478968349571-0.2996385480750.463655054888-0.0862207933555-0.07408944434750.5108511439070.04934374463330.1591439636350.442003828075-0.004177007972060.07546034182690.2894856124470.07796234378920.340225898366-1.45818279404-13.135603135923.1497809124
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 1226 )

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