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- PDB-8h9w: Crystal structure of voltage-gated sodium channel NavAb N49K muta... -

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Basic information

Entry
Database: PDB / ID: 8h9w
TitleCrystal structure of voltage-gated sodium channel NavAb N49K mutant in calcium ion condition
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
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesAliarcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsIrie, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K17795 Japan
Japan Society for the Promotion of Science (JSPS)20K09193 Japan
CitationJournal: Nat Commun / Year: 2023
Title: The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel.
Authors: Irie, K. / Oda, Y. / Sumikama, T. / Oshima, A. / Fujiyoshi, Y.
History
DepositionOct 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)38,52213
Polymers31,3971
Non-polymers7,12512
Water32418
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)154,08852
Polymers125,5894
Non-polymers28,49948
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 area36040 Å2
ΔGint-182 kcal/mol
Surface area50190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.030, 128.030, 202.100
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-1311-

CA

21A-1405-

HOH

31A-1409-

HOH

41A-1412-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#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.) Aliarcobacter butzleri (bacteria) / Gene: Abu_1752 / Production host: Escherichia coli (E. coli) / References: UniProt: A8EVM5
#2: 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, 28 molecules

#3: 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
#4: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 6.54 Å3/Da / Density % sol: 81.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29.81 Å / Num. obs: 23425 / % possible obs: 94.81 % / Redundancy: 26.2 % / Biso Wilson estimate: 69 Å2 / CC1/2: 0.999 / Net I/σ(I): 24.01
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 1270 / CC1/2: 0.883

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUC

5yuc


Resolution: 2.7→29.81 Å / SU ML: 0.3405 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2638 1120 5.03 %
Rwork0.2498 21126 -
obs0.2505 22246 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.21 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 470 18 2304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892331
X-RAY DIFFRACTIONf_angle_d1.15363105
X-RAY DIFFRACTIONf_chiral_restr0.0571354
X-RAY DIFFRACTIONf_plane_restr0.007314
X-RAY DIFFRACTIONf_dihedral_angle_d20.5246983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.3138360.3328524X-RAY DIFFRACTION48.95
2.75-2.80.3841270.3141683X-RAY DIFFRACTION62.06
2.8-2.850.3156480.3007956X-RAY DIFFRACTION86.4
2.85-2.910.3034650.29081072X-RAY DIFFRACTION99.91
2.91-2.970.2791600.29971107X-RAY DIFFRACTION100
2.97-3.040.3019610.25911075X-RAY DIFFRACTION99.91
3.04-3.120.2551580.2581111X-RAY DIFFRACTION100
3.12-3.20.26630.24711084X-RAY DIFFRACTION100
3.2-3.290.2208790.23361081X-RAY DIFFRACTION99.91
3.3-3.40.2124510.22071117X-RAY DIFFRACTION100
3.4-3.520.2544510.2311094X-RAY DIFFRACTION100
3.52-3.660.207620.21251110X-RAY DIFFRACTION100
3.66-3.830.2724440.20761113X-RAY DIFFRACTION100
3.83-4.030.2242430.21911145X-RAY DIFFRACTION100
4.03-4.280.2671660.23071102X-RAY DIFFRACTION100
4.28-4.610.2295560.22911126X-RAY DIFFRACTION100
4.61-5.070.2026680.22061110X-RAY DIFFRACTION100
5.08-5.80.2627540.26651146X-RAY DIFFRACTION100
5.81-7.290.3288590.3161155X-RAY DIFFRACTION99.92
7.3-29.810.3232690.27021215X-RAY DIFFRACTION99.61
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)
14.70087383866-0.155501938370.10655959683.34114838313-1.505127260332.087007166640.2427892272550.211582085103-0.1781753011350.161054603849-0.00849016157245-0.4544067102381.166102929571.18905027360.08308069684860.9772705367470.402578115326-0.2384520980950.9570703711120.1339132396950.82617281736830.354517134-22.583447616628.3659532636
23.709042812980.5077988196151.083113810970.957920303655-0.710208550773.60676805728-0.0103119926842-0.36922414303-0.1492686062350.482618869556-0.091507491709-0.06619254215770.4074831103870.0118528482726-0.1534747557090.6439181858510.04103427547970.008596520190050.3979861492420.06529000050450.517102696016-0.392831783841-16.912766231529.166882825
34.201314539470.462714734005-0.291406378812.444909985330.3104860412364.6467653103-0.0380297866609-0.152567373261-0.06270767100760.0714619993636-0.0922152312554-0.02063406193570.475865734532-0.339088408710.001875494625430.398927925501-0.06530039366490.0651022872010.3456808891870.04002030621480.37648794797-7.92509687707-9.7826583235119.6303856525
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 999 through 1113 )999 - 11131 - 110
22chain 'A' and (resid 1114 through 1152 )1114 - 1152111 - 149
33chain 'A' and (resid 1153 through 1225 )1153 - 1225150 - 222

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