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- PDB-6n4i: Structural basis of Nav1.7 inhibition by a gating-modifier spider... -

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Basic information

Entry
Database: PDB / ID: 6n4i
TitleStructural basis of Nav1.7 inhibition by a gating-modifier spider toxin
Components
  • Beta/omega-theraphotoxin-Tp2a
  • Nav1.7 VSD2-NavAb channel chimera protein
KeywordsMETAL TRANSPORT / sodium channel / toxin / gating-modifier / voltage-gated
Function / homologytoxin activity / lipid binding / pathogenesis / extracellular region / Beta/omega-theraphotoxin-Tp2a
Function and homology information
Biological speciesHomo sapiens (human)
Thrixopelma pruriens (green velvet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.541 Å
AuthorsXu, H. / Koth, C.M. / Payandeh, J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nav1.7 VSD2-NavAb channel chimera protein
B: Nav1.7 VSD2-NavAb channel chimera protein
C: Nav1.7 VSD2-NavAb channel chimera protein
D: Nav1.7 VSD2-NavAb channel chimera protein
E: Beta/omega-theraphotoxin-Tp2a
F: Beta/omega-theraphotoxin-Tp2a
G: Beta/omega-theraphotoxin-Tp2a
H: Beta/omega-theraphotoxin-Tp2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,66124
Polymers149,1738
Non-polymers11,48816
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18970 Å2
ΔGint-173 kcal/mol
Surface area52740 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)221.220, 123.530, 123.990
Angle α, β, γ (deg.)90.00, 124.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nav1.7 VSD2-NavAb channel chimera protein


Mass: 33453.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Protein/peptide
Beta/omega-theraphotoxin-Tp2a / Beta/omega-TRTX-Tp2a / ProTx-II / PT-II / Protoxin-2 / ProTx2


Mass: 3839.687 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thrixopelma pruriens (green velvet) / Production host: synthetic construct (others) / References: UniProt: P83476
#3: Chemical
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM

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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: 4.71 Å3/Da / Density % sol: 73.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.3-2.6M Ammonium sulfate, 100 mM HEPES, pH 7.0; 30% sucrose for cryo
PH range: 4.6-7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 479752 / % possible obs: 99.3 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.43
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.76 / Num. unique obs: 35190 / CC1/2: 0.756 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EK0
Resolution: 3.541→36.892 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.23
RfactorNum. reflection% reflection
Rfree0.2942 1373 4.98 %
Rwork0.2745 --
Obs0.2755 27544 81.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.541→36.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 317 0 8629
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058822
X-RAY DIFFRACTIONf_angle_d0.85411969
X-RAY DIFFRACTIONf_dihedral_angle_d16.6495071
X-RAY DIFFRACTIONf_chiral_restr0.0471374
X-RAY DIFFRACTIONf_plane_restr0.0051396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
3.5409-3.66730.3372200.3568322X-RAY DIFFRACTION10
3.6673-3.8140.2972480.31011146X-RAY DIFFRACTION36
3.814-3.98740.30941180.2912317X-RAY DIFFRACTION72
3.9874-4.19740.30721390.28343102X-RAY DIFFRACTION97
4.1974-4.45990.28871660.26273194X-RAY DIFFRACTION100
4.4599-4.80360.29711960.24763192X-RAY DIFFRACTION100
4.8036-5.28570.27481940.24483194X-RAY DIFFRACTION100
5.2857-6.04770.29051430.31213237X-RAY DIFFRACTION100
6.0477-7.60850.31891630.343221X-RAY DIFFRACTION100
7.6085-36.89360.28671860.25063246X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 99.0797 Å / Origin y: 248.6897 Å / Origin z: 216.8423 Å
111213212223313233
T0.1316 Å2-0.027 Å2-0.0514 Å2-0.2093 Å2-0.0129 Å2--0.1567 Å2
L0.7162 °2-0.2847 °2-0.0014 °2-0.7802 °2-0.0588 °2--0.7156 °2
S-0.1976 Å °-0.0779 Å °-0.1558 Å °-0.0204 Å °0.2219 Å °-0.0585 Å °-0.1775 Å °0.1176 Å °0.0079 Å °
Refinement TLS groupSelection details: all

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