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- PDB-8ha1: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -

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Basic information

Entry
Database: PDB / ID: 8ha1
TitleCrystal structure of voltage-gated sodium channel NavAb N49K/L176G 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: 3.5 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)38,47214
Polymers31,3411
Non-polymers7,13113
Water23413
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)153,88756
Polymers125,3654
Non-polymers28,52252
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 area30110 Å2
ΔGint-199 kcal/mol
Surface area51110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.910, 126.910, 201.780
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-

NA

21A-1313-

NA

31A-1406-

HOH

41A-1413-

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, 24 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 80.98 % / 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: 3.5→29.97 Å / Num. obs: 10747 / % possible obs: 96.59 % / Redundancy: 39.8 % / Biso Wilson estimate: 152.11 Å2 / CC1/2: 1 / Net I/σ(I): 20.78
Reflection shellResolution: 3.5→3.6 Å / Num. unique obs: 728 / CC1/2: 0.56

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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: 3.5→29.91 Å / SU ML: 0.5001 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 33.5777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2967 504 4.84 %
Rwork0.2913 9906 -
obs0.2916 10410 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.29 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 472 14 2301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382331
X-RAY DIFFRACTIONf_angle_d0.73543106
X-RAY DIFFRACTIONf_chiral_restr0.0463354
X-RAY DIFFRACTIONf_plane_restr0.0044315
X-RAY DIFFRACTIONf_dihedral_angle_d19.0866985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.560.511490.5245203X-RAY DIFFRACTION39.41
3.56-3.630.4166280.4491487X-RAY DIFFRACTION98.66
3.63-3.690.3571220.3803486X-RAY DIFFRACTION100
3.7-3.770.3563230.3378518X-RAY DIFFRACTION100
3.77-3.850.2629190.3327510X-RAY DIFFRACTION100
3.85-3.940.3152200.2961504X-RAY DIFFRACTION100
3.94-4.040.2604200.2678498X-RAY DIFFRACTION100
4.04-4.150.3436290.2761501X-RAY DIFFRACTION100
4.15-4.270.33280.2861502X-RAY DIFFRACTION100
4.27-4.410.3047280.276506X-RAY DIFFRACTION100
4.41-4.560.2322250.2927503X-RAY DIFFRACTION100
4.57-4.750.227240.2783498X-RAY DIFFRACTION100
4.75-4.960.2443390.2674504X-RAY DIFFRACTION100
4.96-5.220.3024230.2692513X-RAY DIFFRACTION100
5.22-5.550.3181290.3096511X-RAY DIFFRACTION100
5.55-5.970.303220.3214518X-RAY DIFFRACTION100
5.97-6.570.3805280.3461514X-RAY DIFFRACTION100
6.57-7.50.2437280.3099536X-RAY DIFFRACTION100
7.51-9.380.2801360.2238517X-RAY DIFFRACTION100
9.42-29.910.3346240.292577X-RAY DIFFRACTION99.17
Refinement TLS params.Method: refined / Origin x: 11.7692848821 Å / Origin y: -16.7295059191 Å / Origin z: 25.7358184079 Å
111213212223313233
T1.16893111716 Å20.0552461200071 Å2-0.0652746011946 Å2-0.622710342158 Å20.207592549604 Å2--1.0300132488 Å2
L3.69597880226 °2-1.34772328553 °21.09325250657 °2-2.28754244449 °20.628590147113 °2--3.66694721989 °2
S-0.284010435826 Å °-0.115177503585 Å °-0.0017533722355 Å °0.627244237743 Å °0.151096552793 Å °-0.376109376433 Å °0.895693561234 Å °0.640088806208 Å °0.0586963473743 Å °
Refinement TLS groupSelection details: all

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