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- PDB-8h9o: Crystal structure of voltage-gated sodium channel NavAb N49K muta... -

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Basic information

Entry
Database: PDB / ID: 8h9o
TitleCrystal structure of voltage-gated sodium channel NavAb N49K mutant in sodium 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.
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)39,18414
Polymers31,3971
Non-polymers7,78713
Water28816
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)156,73556
Polymers125,5894
Non-polymers31,14652
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 area47150 Å2
ΔGint-221 kcal/mol
Surface area51160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.830, 127.830, 200.910
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-

NA

21A-1404-

HOH

31A-1413-

HOH

41A-1414-

HOH

51A-1416-

HOH

61A-1417-

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, 27 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.: 9 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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 % / Description: Pyramidal shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→29.66 Å / Num. obs: 12883 / % possible obs: 99.66 % / Redundancy: 14.4 % / Biso Wilson estimate: 81.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.0186 / Net I/σ(I): 24.82
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 0.8552 / Num. unique obs: 1260 / CC1/2: 0.945 / Rpim(I) all: 0.2298

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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: 3.3→29.66 Å / SU ML: 0.1411 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.0993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 617 4.79 %
Rwork0.2552 12260 -
obs0.256 12877 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.53 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 517 17 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172404
X-RAY DIFFRACTIONf_angle_d1.6363195
X-RAY DIFFRACTIONf_chiral_restr0.088358
X-RAY DIFFRACTIONf_plane_restr0.0074322
X-RAY DIFFRACTIONf_dihedral_angle_d20.54891034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.360.2292300.2999602X-RAY DIFFRACTION99.84
3.36-3.420.3224210.2863607X-RAY DIFFRACTION100
3.42-3.480.2131330.273592X-RAY DIFFRACTION100
3.48-3.550.2906300.2339613X-RAY DIFFRACTION100
3.55-3.630.3544300.2388595X-RAY DIFFRACTION100
3.63-3.720.2829290.2397594X-RAY DIFFRACTION100
3.72-3.810.3582250.2401601X-RAY DIFFRACTION100
3.81-3.910.2327270.2279614X-RAY DIFFRACTION100
3.91-4.030.2368220.22622X-RAY DIFFRACTION100
4.03-4.150.2807310.213591X-RAY DIFFRACTION100
4.16-4.30.2877380.2571604X-RAY DIFFRACTION100
4.3-4.480.2273310.2332613X-RAY DIFFRACTION100
4.48-4.680.1981310.2184607X-RAY DIFFRACTION99.84
4.68-4.920.2004380.2186616X-RAY DIFFRACTION100
4.92-5.230.2819340.2379605X-RAY DIFFRACTION100
5.23-5.630.2507330.2765621X-RAY DIFFRACTION99.85
5.64-6.190.385260.3187620X-RAY DIFFRACTION100
6.2-7.080.3836370.3157626X-RAY DIFFRACTION100
7.08-8.880.2721360.2569634X-RAY DIFFRACTION100
8.88-29.660.2905350.2837683X-RAY DIFFRACTION98.9
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)
12.71953234401-0.2511251246930.8302663454023.3264449252-1.701459788322.007036064330.01159850670660.0772877971798-0.04602713908630.233316671498-0.181901950352-0.7035323913481.185918271181.380819378420.1064079515630.7529764200970.592384069988-0.2344404530190.9944993662870.2484274906660.97197842773132.0021802274-22.91713985729.4939541272
27.043991910921.531604660972.176652435951.89983118851-1.035840824613.04927820808-0.2204848924610.296003291345-0.1686836930330.2894945509-0.1664378845-0.4406832999810.4343280474090.6127126358840.385396753740.6206324204140.2037893635860.02433977917550.311833900420.05457949516390.6234264906218.48521719965-18.754348762726.2381504985
32.51782034293-1.18463197592-1.6448637514.42446176015-0.4691937805238.33347064203-0.0819952011188-0.381930492783-0.4089808844650.211620332957-0.209633552615-0.0423915670510.3201314849340.024367392880.273768695680.206199532802-0.1542385234570.04973908315770.264754600630.08751850636690.556067419733-7.82788818415-9.783317726920.0324895429
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 1088 )999 - 10881 - 90
22chain 'A' and (resid 1089 through 1152 )1089 - 115291 - 151
33chain 'A' and (resid 1153 through 1226 )1153 - 1226152 - 225

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