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- PDB-8ha2: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -

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Basic information

Entry
Database: PDB / ID: 8ha2
TitleCrystal structure of voltage-gated sodium channel NavAb N49K/L176G 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: 3.3 Å
AuthorsIrie, K. / Oda, Y.
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 26, 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)38,50614
Polymers31,3411
Non-polymers7,16513
Water19811
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)154,02456
Polymers125,3654
Non-polymers28,65952
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 area52240 Å2
ΔGint-276 kcal/mol
Surface area48260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.130, 127.130, 200.550
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-1312-

CA

21A-1403-

HOH

31A-1408-

HOH

41A-1411-

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: 31341.174 Da / Num. of mol.: 1 / Mutation: N49K, L176G
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, 22 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.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 6.46 Å3/Da / Density % sol: 80.97 % / Description: Pyramidal shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25mM 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 EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→29.96 Å / Num. obs: 12718 / % possible obs: 92.63 % / Redundancy: 40.1 % / Biso Wilson estimate: 85.09 Å2 / CC1/2: 1 / Net I/σ(I): 19.61
Reflection shellResolution: 3.3→3.4 Å / Num. unique obs: 472 / CC1/2: 0.839

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Processing

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

5yuc


Resolution: 3.3→29.96 Å / SU ML: 0.3379 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.0477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.281 571 4.83 %
Rwork0.2612 11242 -
obs0.2622 11813 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 472 11 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00942294
X-RAY DIFFRACTIONf_angle_d1.3113056
X-RAY DIFFRACTIONf_chiral_restr0.0627347
X-RAY DIFFRACTIONf_plane_restr0.0055309
X-RAY DIFFRACTIONf_dihedral_angle_d22.2067971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.360.52880.3349178X-RAY DIFFRACTION30.05
3.36-3.420.1958140.3046272X-RAY DIFFRACTION46.81
3.42-3.480.3138230.2568464X-RAY DIFFRACTION77.3
3.48-3.550.2183300.2502591X-RAY DIFFRACTION99.84
3.55-3.630.2185350.2266596X-RAY DIFFRACTION100
3.63-3.720.3414220.2597586X-RAY DIFFRACTION100
3.72-3.810.2704240.2484614X-RAY DIFFRACTION100
3.81-3.910.2821290.2371589X-RAY DIFFRACTION99.84
3.91-4.030.2241210.2141602X-RAY DIFFRACTION100
4.03-4.160.1973340.2029601X-RAY DIFFRACTION100
4.16-4.30.2752370.2293596X-RAY DIFFRACTION100
4.3-4.480.2416240.2427604X-RAY DIFFRACTION100
4.48-4.680.2159340.2179599X-RAY DIFFRACTION99.84
4.68-4.920.2343370.2217591X-RAY DIFFRACTION100
4.93-5.230.2752330.2454610X-RAY DIFFRACTION100
5.23-5.630.2946340.2871613X-RAY DIFFRACTION99.85
5.63-6.20.3904260.3145610X-RAY DIFFRACTION100
6.2-7.080.3695350.337624X-RAY DIFFRACTION100
7.08-8.880.3263360.2686625X-RAY DIFFRACTION100
8.89-29.960.3288350.3147677X-RAY DIFFRACTION99.58
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)
12.13030569535-0.603493761153.001477275588.28983829162-5.063550897826.419921506050.400148839455-0.14460465661-0.7754802829310.240136102973-0.326448709713-0.7664951541860.7801519234530.589545473875-0.07589042802321.923187170191.05012709654-0.3895171253722.005065181350.662201217471.1412570827838.6878390189-28.219743725645.5244390668
25.48837584825-1.834140965173.931347120834.90354321377-3.184249504983.67821275123-0.2542170689850.6865329340340.4208171308870.507246250557-0.00102024065047-1.292559264670.5185381059511.830260557810.4055687810230.9162752407810.530847575625-0.2244811321231.243088595810.1280147225221.0659534963134.9091501093-18.839997859923.9374632662
33.82483464108-1.038258432022.329559936842.88577323939-2.920201988563.47306453185-0.354938983833-0.403263299202-0.49237228507-0.1013840600340.358459690940.1131322225981.973394993651.590057210820.03719505852171.253580640960.433131088805-0.2278337907550.9010763650280.2272001092571.0361722378521.9229210819-22.301189764330.7830007854
41.47340556088-1.643922950250.9461956588122.32432635303-3.042139295428.90155507639-0.0979449761689-0.20730738784-0.4305317028640.3641538168480.1760872288450.155696940790.97815812787-0.562832692674-0.1137489787320.640549187683-0.1154344213940.1529682274140.3415845316770.09436395476960.533953381993-8.76837376061-18.944622696623.7062197441
59.35141108817-3.610992586393.9916196179.82538217006-2.250189719149.583237163710.006666463814931.19716342024-0.699834658041-1.605772951810.35053962415-0.4279612804191.28107513069-0.21379549722-0.3108055544260.931601716806-0.210996725240.1891527687630.427581306425-0.01581914858520.37996839926-8.76958883649-17.24555561715.86912314965
66.02022522647-2.448727938870.8608029854771.023588354350.1260069154366.41870288504-0.167456457569-0.0362726874059-0.4461218008320.161511497194-0.02173656111130.05136361406750.4025115723240.3483371764440.2297562519280.427062532735-0.1122103353960.1385545356870.3135394686350.07709047833440.517760382989-4.57111615798-10.864722195414.6172664529
73.444728016070.517575657752-1.075927306074.521965430141.224371864989.741663978180.0806317879726-0.604765399783-0.1940047474790.449308961068-0.0511605312528-0.03594304137990.651891576986-0.657006951919-0.07483107335050.302434674883-0.138389307670.0984778793420.4430755798090.01008225391430.348441054656-10.9546401014-7.760894588222.0154087639
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 1011 )999 - 10111 - 13
22chain 'A' and (resid 1012 through 1066 )1012 - 106614 - 68
33chain 'A' and (resid 1067 through 1127 )1067 - 112769 - 125
44chain 'A' and (resid 1128 through 1152 )1128 - 1152126 - 150
55chain 'A' and (resid 1153 through 1162 )1153 - 1162151 - 160
66chain 'A' and (resid 1163 through 1183 )1163 - 1183161 - 181
77chain 'A' and (resid 1184 through 1220 )1184 - 1220182 - 218

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