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- PDB-8dj1: Crystal structure of NavAb V126T as a basis for the human Nav1.7 ... -

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Basic information

Entry
Database: PDB / ID: 8dj1
TitleCrystal structure of NavAb V126T as a basis for the human Nav1.7 Inherited Erythromelalgia S241T mutation
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / Voltage-gated sodium channel Ion transport protein
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 cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesAliarcobacter butzleri RM4018 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWisedchaisri, G. / Gamal El-Din, T.M. / Zheng, N. / Catterall, W.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS015751 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35 NS111573 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL112808 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural basis for severe pain caused by mutations in the S4-S5 linkers of voltage-gated sodium channel Na V 1.7.
Authors: Wisedchaisri, G. / Gamal El-Din, T.M. / Zheng, N. / Catterall, W.A.
History
DepositionJun 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4168
Polymers29,7911
Non-polymers4,6247
Water724
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)137,66332
Polymers119,1654
Non-polymers18,49828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area41450 Å2
ΔGint-250 kcal/mol
Surface area42200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.441, 123.441, 191.074
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

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Components

#1: Protein Ion transport protein


Mass: 29791.270 Da / Num. of mol.: 1 / Mutation: V126T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliarcobacter butzleri RM4018 (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


Mass: 678.940 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 6.11 Å3/Da / Density % sol: 79.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 1.8 M Ammonium Sulfate 0.1 M Sodium Citrate pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2021
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13526 / % possible obs: 98.6 % / Redundancy: 6 % / Biso Wilson estimate: 60.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.059 / Net I/σ(I): 12.8
Reflection shellResolution: 3.1→3.15 Å / Rmerge(I) obs: 1.917 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 659 / CC1/2: 0.479 / Rpim(I) all: 0.891

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Processing

Software
NameVersionClassification
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MWA

6mwa


Resolution: 3.1→39.7 Å / SU ML: 0.3562 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.9322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 561 4.9 %
Rwork0.2136 10898 -
obs0.2157 11459 83.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.31 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 218 4 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252207
X-RAY DIFFRACTIONf_angle_d0.55382990
X-RAY DIFFRACTIONf_chiral_restr0.0434357
X-RAY DIFFRACTIONf_plane_restr0.0049332
X-RAY DIFFRACTIONf_dihedral_angle_d10.7415423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.420.3399870.26091299X-RAY DIFFRACTION41.25
3.42-3.910.26431600.21623028X-RAY DIFFRACTION94.77
3.91-4.920.23381580.18773231X-RAY DIFFRACTION99.01
4.92-39.70.25881560.22763340X-RAY DIFFRACTION97.52

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