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- PDB-4ekw: Crystal structure of the NavAb voltage-gated sodium channel (wild... -

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Basic information

Entry
Database: PDB / ID: 4ekw
TitleCrystal structure of the NavAb voltage-gated sodium channel (wild-type, 3.2 A)
ComponentsIon transport proteinIon transporter
KeywordsTRANSPORT PROTEIN / voltage-gated ion channel / tetrameric ion channel superfamily / voltage-gated sodium channel / membrane
Function / homology
Function and homology information


monoatomic cation channel activity / identical protein binding / plasma membrane
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
PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsPayandeh, J. / Gamal El-Din, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of a voltage-gated sodium channel in two potentially inactivated states.
Authors: Payandeh, J. / Gamal El-Din, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,67413
Polymers134,8994
Non-polymers3,7759
Water543
1
A: Ion transport protein
B: Ion transport protein
hetero molecules

A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,35214
Polymers134,8994
Non-polymers4,45410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area15060 Å2
ΔGint-151 kcal/mol
Surface area47950 Å2
MethodPISA
2
C: Ion transport protein
D: Ion transport protein
hetero molecules

C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,99512
Polymers134,8994
Non-polymers3,0968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area14640 Å2
ΔGint-169 kcal/mol
Surface area47140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.856, 125.856, 192.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
Ion transport protein / Ion transporter


Mass: 33724.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 5.65 Å3/Da / Density % sol: 78.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: CHAPSO:DMPC BICELLES, 2 M AMMONIUM SULPHATE, 0.1 M NA-CITRATE, 28% GLUCOSE, NICOTINIC ACID, pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2011
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.496
11K, H, -L20.504
ReflectionResolution: 3.21→50 Å / Num. all: 44951 / Num. obs: 44951 / % possible obs: 96.44 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.086
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.2-3.262.90.6761.05199.4
3.26-3.3130.4921.48199.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RVY
Resolution: 3.21→50 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.822 / SU B: 35.53 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.32168 2397 5.1 %RANDOM
Rwork0.3079 ---
all0.30861 44951 --
obs0.30861 44951 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 102.725 Å2
Baniso -1Baniso -2Baniso -3
1-53.81 Å20 Å20 Å2
2--53.81 Å20 Å2
3----107.63 Å2
Refinement stepCycle: LAST / Resolution: 3.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7138 0 77 3 7218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027410
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.97910076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.96821.489282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.899151111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3231540
X-RAY DIFFRACTIONr_chiral_restr0.0810.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215312
LS refinement shellResolution: 3.206→3.289 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 176 -
Rwork0.227 3321 -
obs--96.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2161-0.4631-1.94860.33870.9123.3358-0.0047-0.0087-0.37490.0372-0.123-0.20890.03080.03720.12770.77210.22590.10660.8455-0.09761.195832.101738.366861.5445
20.1066-0.0095-0.02912.15140.05993.5680.11680.1672-0.1379-0.1867-0.16880.1594-0.0695-0.06310.0520.30990.05610.11420.7032-0.05761.14319.561862.531665.1412
34.69814.218-2.39066.6901-6.38787.58890.1598-0.00590.0999-0.1801-0.0097-0.11610.598-0.1514-0.15010.6531-0.0299-0.01350.6892-0.14741.253510.607271.377273.842
40.82010.4732-2.93263.81671.440113.41780.15770.14550.2295-0.16680.7447-0.3011-0.64840.2451-0.90230.30210.0430.0770.85120.00231.22914.856576.497767.0676
51.4354-0.4319-2.54114.08035.766713.7510.02580.0291-0.5303-0.25610.05680.2379-0.04260.4148-0.08260.54230.0124-0.17840.74210.00121.2574-29.01235.918261.008
64.08961.0102-1.22171.9375-1.44911.4434-0.04730.52890.0061-0.08730.12490.32750.0945-0.4276-0.07750.7118-0.0766-0.13850.4798-0.18481.1089-13.697735.196356.8852
70.312-0.01760.65651.3191-0.28371.46970.07080.07320.0374-0.0754-0.0695-0.36660.06470.0714-0.00130.54510.21450.05790.6688-0.00231.268413.236452.85875.2797
83.578-3.1456-2.11092.79571.84581.2561-0.1305-0.2066-0.1676-0.04830.19760.28260.02110.1046-0.06710.9159-0.2882-0.00020.71710.01411.300711.900859.102760.2547
90.3008-0.18070.56551.3834-1.36282.18650.1741-0.04330.2627-0.2485-0.335-0.43920.72570.09420.16090.8896-0.2117-0.19830.9483-0.14971.433232.454285.3752114.1325
100.07080.1356-0.39560.5071-1.26193.2652-0.0866-0.10040.01070.1054-0.0473-0.1589-0.0810.30910.13390.55670.0075-0.22370.7915-0.13591.347918.212863.8224118.0449
110.6785-1.02120.5371.5832-1.03293.1423-0.038-0.1859-0.06580.05540.20130.2220.2583-0.3595-0.16330.6064-0.069-0.0550.546-0.03141.189910.02852.872799.1689
121.8275-0.7877-0.58183.9009-0.22690.264-0.1554-0.2185-0.04880.27230.247-0.03660.0516-0.0066-0.09150.5402-0.06890.03030.60340.07821.15973.017248.5188106.697
131.9671-1.5373-0.7471.69450.56890.28840.0102-0.24060.1215-0.11580.02280.3393-0.0440.0908-0.0330.78060.19990.08010.7882-0.11171.119-23.259294.0033117.8833
141.51740.2737-1.35110.2297-0.89823.62110.0481-0.3743-0.18810.04730.09680.0273-0.3117-0.1781-0.14490.6158-0.1072-0.00990.4618-0.20191.2372-2.397785.0965112.4988
154.14563.9094.4856.15934.50844.88950.1623-0.3186-0.00320.706-0.011-1.28380.2127-0.3606-0.15130.833-0.0510.12920.5262-0.08661.06939.400972.275899.3869
161.3578-1.22241.09851.1388-0.98360.8911-0.0636-0.2343-0.09590.05320.08870.058-0.067-0.2111-0.02510.6102-0.3-0.02720.7394-0.02361.25613.636167.5415109.5248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1001 - 1094
2X-RAY DIFFRACTION2A1095 - 1159
3X-RAY DIFFRACTION3A1160 - 1181
4X-RAY DIFFRACTION4A1182 - 1219
5X-RAY DIFFRACTION5B1001 - 1049
6X-RAY DIFFRACTION6B1050 - 1137
7X-RAY DIFFRACTION7B1138 - 1193
8X-RAY DIFFRACTION8B1194 - 1219
9X-RAY DIFFRACTION9C1001 - 1104
10X-RAY DIFFRACTION10C1105 - 1150
11X-RAY DIFFRACTION11C1151 - 1184
12X-RAY DIFFRACTION12C1185 - 1213
13X-RAY DIFFRACTION13D1001 - 1080
14X-RAY DIFFRACTION14D1081 - 1155
15X-RAY DIFFRACTION15D1156 - 1187
16X-RAY DIFFRACTION16D1188 - 1217

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