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- PDB-8h9y: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -

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Basic information

Entry
Database: PDB / ID: 8h9y
TitleCrystal structure of voltage-gated sodium channel NavAb N49K/L176Q 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: 3.4 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 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)38,57714
Polymers31,4121
Non-polymers7,16513
Water21612
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)154,30856
Polymers125,6494
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 area52270 Å2
ΔGint-303 kcal/mol
Surface area49070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.940, 127.940, 201.920
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-1313-

CA

21A-1404-

HOH

31A-1408-

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: 31412.252 Da / Num. of mol.: 1 / Mutation: N49K, L176Q
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, 23 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.: 12 / 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: 6.58 Å3/Da / Density % sol: 81.3 % / 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, 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 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: 3.4→29.78 Å / Num. obs: 11874 / % possible obs: 92.05 % / Redundancy: 89 % / Biso Wilson estimate: 59.63 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.87
Reflection shellResolution: 3.4→3.5 Å / Num. unique obs: 446 / CC1/2: 0.826

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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: 3.4→29.78 Å / SU ML: 0.3827 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.4084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2636 532 4.85 %
Rwork0.2541 10432 -
obs0.2545 10964 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.47 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 472 12 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992367
X-RAY DIFFRACTIONf_angle_d1.24313154
X-RAY DIFFRACTIONf_chiral_restr0.0617358
X-RAY DIFFRACTIONf_plane_restr0.0063322
X-RAY DIFFRACTIONf_dihedral_angle_d23.6277998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.460.174670.2904180X-RAY DIFFRACTION32.3
3.46-3.520.3130.2761246X-RAY DIFFRACTION45.92
3.52-3.590.2608170.2714373X-RAY DIFFRACTION66.55
3.59-3.660.3145370.2639540X-RAY DIFFRACTION98.3
3.66-3.740.3027210.2526555X-RAY DIFFRACTION100
3.74-3.830.309220.2666555X-RAY DIFFRACTION99.83
3.83-3.920.2422240.2494561X-RAY DIFFRACTION100
3.92-4.030.1984190.2171576X-RAY DIFFRACTION100
4.03-4.150.1684300.2061544X-RAY DIFFRACTION100
4.15-4.280.2433350.2259554X-RAY DIFFRACTION100
4.28-4.430.2541290.2296571X-RAY DIFFRACTION100
4.44-4.610.2349270.2125567X-RAY DIFFRACTION100
4.61-4.820.2269340.2173551X-RAY DIFFRACTION99.66
4.82-5.070.273340.2364547X-RAY DIFFRACTION100
5.07-5.390.2206300.2512570X-RAY DIFFRACTION100
5.39-5.80.2963240.32574X-RAY DIFFRACTION100
5.8-6.380.3572340.3262567X-RAY DIFFRACTION100
6.38-7.290.3394260.3135588X-RAY DIFFRACTION100
7.29-9.140.2825390.2232581X-RAY DIFFRACTION99.84
9.15-29.780.2835300.2895632X-RAY DIFFRACTION99.4
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)
12.82262821834-0.2496954238990.6670690809741.6188343281-0.5111399062682.179095432310.0312657836595-0.0161896196297-0.1043912322680.370274433353-0.155826665854-0.6149938015960.3155990357080.4222830416390.246409947440.5046632951790.34238264267-0.2240176871880.7463666960580.2411055908670.60285442721235.5605477174-17.81760420828.7551501019
24.04836291366-2.167346722341.40290640824.07482724243-1.674777404652.673683842690.2645939734370.6845735154180.0469276659963-0.308629804947-0.29387523991-0.1021472871110.1290550229480.3251366081540.1202273893180.7211585176760.549332266247-0.1798200659390.8022234856480.06160313827110.68808353741335.6306062634-24.804154914626.3709433871
34.22949988134-2.339106050411.628821245764.75636472938-2.317705265491.2075671450.5912460686540.468886007485-0.865597830028-1.35449334613-0.4937300901850.1093448744641.304062831990.581407565018-0.2111290709471.374400220430.480067728482-0.2865921487390.8051707330750.1542994977210.73487802261124.0385773117-28.815856606129.8798562735
47.44926350787-0.3257949345873.917256640573.84371895441-1.002797770967.70140932130.4036440606490.492961183814-0.671957955602-0.244747810614-0.166415151322-0.6273105482231.524735829771.04443404182-0.261581853220.7199302411120.220035745768-0.06540185100230.4478332470810.2157774263040.57134181196923.8025048536-19.709286325123.5578057402
51.075534796660.459661354596-0.137824886631.609593031860.6486400954151.06371396323-0.0680153437386-0.257017322771-0.1355621280760.383207779648-0.0801663172781-0.2142529524940.4490931634920.181462838878-0.007843072583470.276820932981-0.1201923801150.0254956456320.239574364980.1463343588430.201939007079-0.214555337583-17.012777785929.1065100555
60.0299957159260.306855215919-0.2791440219564.07163519715-1.327863562664.97187265804-0.1196951482260.0728080844837-0.116714079266-0.181145490635-0.00556116495511-0.1090942148190.383318067003-0.1251957061080.1015776044540.315566325108-0.1727620092490.1434888879460.155366648048-0.02468943853550.105678493743-8.91883470738-17.26554487925.91872468443
70.8466052152090.603629617722-0.3705998539711.44479762133-0.3595673541551.01708776813-0.1493998940540.0473178708953-0.227714915726-0.0496063016701-0.005432076774270.1249444233170.206528753945-0.125664896912-0.580848903506-0.0516986258024-0.1829232842940.148551931795-0.08013210349710.06071850818280.0945936154665-8.58087057546-9.448067990812.255798331
82.82587767573-0.841871411584-0.1840466419913.225453614150.1050451866992.50000029514-0.103710178747-0.691965085240.00925820501920.842998044165-0.0355190271668-0.4269751417540.01309318389470.4516237925170.1380104506720.289162672216-0.12669898660.0303996439910.3910083260610.1788503878030.136322435126-6.45521697466-7.6352103510832.4825869912
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 1041 )999 - 10411 - 42
22chain 'A' and (resid 1042 through 1066 )1042 - 106643 - 67
33chain 'A' and (resid 1067 through 1095 )1067 - 109568 - 96
44chain 'A' and (resid 1096 through 1113 )1096 - 111397 - 114
55chain 'A' and (resid 1114 through 1152 )1114 - 1152115 - 153
66chain 'A' and (resid 1153 through 1162 )1153 - 1162154 - 163
77chain 'A' and (resid 1163 through 1193 )1163 - 1193164 - 194
88chain 'A' and (resid 1194 through 1226 )1194 - 1226195 - 227

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