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- PDB-8div: Crystal structure of NavAb I22V as a basis for the human Nav1.7 I... -

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Basic information

Entry
Database: PDB / ID: 8div
TitleCrystal structure of NavAb I22V as a basis for the human Nav1.7 Inherited Erythromelalgia I136V mutation
ComponentsIon transport proteinIon transporter
KeywordsMEMBRANE PROTEIN / Voltage-gated sodium channel Ion transport protein
Function / homology
Function and homology information


monoatomic cation channel activity / identical protein binding / plasma membrane
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
beta-D-glucopyranose / 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: 2.54 Å
AuthorsWisedchaisri, G. / Gamal El-Din, T.M. / Powell, N.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: J.Gen.Physiol. / Year: 2023
Title: Structural basis for severe pain caused by mutations in the voltage sensors of sodium channel NaV1.7.
Authors: Wisedchaisri, G. / Gamal El-Din, T.M. / Powell, N.M. / Zheng, N. / Catterall, W.A.
History
DepositionJun 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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)34,5809
Polymers29,7751
Non-polymers4,8058
Water41423
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)138,32036
Polymers119,1014
Non-polymers19,21832
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 area44410 Å2
ΔGint-218 kcal/mol
Surface area44880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.578, 124.578, 190.927
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 / Ion transporter


Mass: 29775.270 Da / Num. of mol.: 1 / Mutation: I22V
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: 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
#4: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 6.22 Å3/Da / Density % sol: 80.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.7-1.8 M Ammonium sulfate 0.1 M Sodium Citrate pH 5.0

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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: Mar 7, 2009
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: 2.53→50 Å / Num. obs: 22384 / % possible obs: 87.6 % / Redundancy: 11.5 % / Biso Wilson estimate: 37.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.045 / Net I/σ(I): 13.3
Reflection shellResolution: 2.53→2.57 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 0.43 / Num. unique obs: 415 / CC1/2: 0.886 / Rpim(I) all: 0.36 / % possible all: 33.3

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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: 3RVY

3rvy


Resolution: 2.54→41.97 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 942 5.32 %
Rwork0.1993 16770 -
obs0.2013 17712 70.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.03 Å2
Refinement stepCycle: LAST / Resolution: 2.54→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 264 23 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892283
X-RAY DIFFRACTIONf_angle_d1.07153085
X-RAY DIFFRACTIONf_chiral_restr0.0598364
X-RAY DIFFRACTIONf_plane_restr0.009340
X-RAY DIFFRACTIONf_dihedral_angle_d14.3937463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.670.2256190.2201344X-RAY DIFFRACTION10.38
2.67-2.840.262480.224843X-RAY DIFFRACTION25.19
2.84-3.060.2804990.22721894X-RAY DIFFRACTION56.51
3.06-3.370.25762090.22413266X-RAY DIFFRACTION97.01
3.37-3.850.21981730.17853413X-RAY DIFFRACTION100
3.85-4.850.22421890.16923427X-RAY DIFFRACTION99.97
4.85-41.970.23772050.22163583X-RAY DIFFRACTION99.55

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