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- PDB-8ech: Tick-borne encephalitis virus capsid protein NLS bound to host im... -

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Basic information

Entry
Database: PDB / ID: 8ech
TitleTick-borne encephalitis virus capsid protein NLS bound to host importin alpha 2
Components
  • Capsid protein C
  • Importin subunit alpha-1
KeywordsVIRAL PROTEIN / bipartite / nuclear import / capsid
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / viral capsid / host cell ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / viral capsid / host cell / DNA-binding transcription factor binding / protein dimerization activity / postsynaptic density / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / glutamatergic synapse / virion membrane / structural molecule activity / extracellular region / nucleoplasm / membrane / cytosol
Similarity search - Function
Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats ...Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Armadillo-like helical / Immunoglobulin E-set / Armadillo-type fold
Similarity search - Domain/homology
Polyprotein / Importin subunit alpha-1
Similarity search - Component
Biological speciesTick-borne encephalitis virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRoby, J.A. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure and biological functions of tick-borne encephalitis virus capsid protein
Authors: Selinger, M. / Novotny, R. / Sys, J. / Roby, J.A. / Tykalova, H. / Ranjani, G.S. / Vancova, M. / Jaklova, K. / Kaufman, F. / Bloom, M.E. / Zdrahal, Z. / Grubhoffer, L. / Forwood, J.K. / ...Authors: Selinger, M. / Novotny, R. / Sys, J. / Roby, J.A. / Tykalova, H. / Ranjani, G.S. / Vancova, M. / Jaklova, K. / Kaufman, F. / Bloom, M.E. / Zdrahal, Z. / Grubhoffer, L. / Forwood, J.K. / Hrabal, R. / Rumlova, M. / Sterba, J.
History
DepositionSep 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
C: Capsid protein C
E: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)57,8472
Polymers57,8472
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint5 kcal/mol
Surface area18470 Å2
Unit cell
Length a, b, c (Å)78.209, 90.050, 99.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Capsid protein C


Mass: 2578.204 Da / Num. of mol.: 1 / Fragment: residues 76-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M1LJY4
#2: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55268.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.7 M sodium citrate, 0.1 M HEPES, pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→29.52 Å / Num. obs: 44694 / % possible obs: 100 % / Redundancy: 12 % / Rpim(I) all: 0.039 / Net I/σ(I): 8.7
Reflection shellResolution: 2.05→2.11 Å / Num. unique obs: 3429 / Rpim(I) all: 0.33

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Processing

Software
NameVersionClassification
PHENIX(1.19rc4_4035: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bw0

6bw0


Resolution: 2.05→29.52 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 2208 4.95 %
Rwork0.1931 --
obs0.1945 44587 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 0 162 3507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023401
X-RAY DIFFRACTIONf_angle_d0.5484622
X-RAY DIFFRACTIONf_dihedral_angle_d13.2651256
X-RAY DIFFRACTIONf_chiral_restr0.037555
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.37041300.34232633X-RAY DIFFRACTION100
2.09-2.140.33781140.32604X-RAY DIFFRACTION100
2.14-2.20.34341310.26092629X-RAY DIFFRACTION100
2.2-2.260.29091470.23142610X-RAY DIFFRACTION100
2.26-2.320.22381410.21352579X-RAY DIFFRACTION100
2.32-2.40.30781360.21112630X-RAY DIFFRACTION100
2.4-2.480.26661200.21342645X-RAY DIFFRACTION100
2.48-2.580.2451300.21722634X-RAY DIFFRACTION100
2.58-2.70.24631390.22272616X-RAY DIFFRACTION100
2.7-2.840.23431460.20572630X-RAY DIFFRACTION100
2.84-3.020.19821350.21772666X-RAY DIFFRACTION100
3.02-3.250.28211240.22282650X-RAY DIFFRACTION100
3.25-3.580.23651400.19732659X-RAY DIFFRACTION100
3.58-4.10.17281360.16242717X-RAY DIFFRACTION100
4.1-5.160.16731570.14882679X-RAY DIFFRACTION100
5.16-29.520.2041820.17122798X-RAY DIFFRACTION100

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