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- PDB-5fc8: Mouse importin alpha: Dengue 3 NS5 C-terminal NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 5fc8
TitleMouse importin alpha: Dengue 3 NS5 C-terminal NLS peptide complex
Components
  • Importin subunit alpha-1
  • Nonstructural protein 5
KeywordsPROTEIN TRANSPORT/Viral Protein / Dengue / NS5 / Importin / PROTEIN TRANSPORT-Viral Protein complex
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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule ...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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / RNA-dependent RNA polymerase activity / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / DNA/RNA polymerase superfamily / Mainly Alpha
Similarity search - Domain/homology
Nonstructural protein 5 / Importin subunit alpha-1
Similarity search - Component
Biological speciesDengue virus 3
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSmith, K.M. / Forwood, J.K.
CitationJournal: PLoS Pathog. / Year: 2016
Title: The C-terminal 18 Amino Acid Region of Dengue Virus NS5 Regulates its Subcellular Localization and Contains a Conserved Arginine Residue Essential for Infectious Virus Production.
Authors: Tay, M.Y. / Smith, K. / Ng, I.H. / Chan, K.W. / Zhao, Y. / Ooi, E.E. / Lescar, J. / Luo, D. / Jans, D.A. / Forwood, J.K. / Vasudevan, S.G.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Nonstructural protein 5
E: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)59,5632
Polymers59,5632
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-5 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.940, 89.880, 100.370
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 Nonstructural protein 5


Mass: 4294.840 Da / Num. of mol.: 1 / Fragment: UNP residues 50-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6VDJ7
#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 / Fragment: UNP residues 71-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52293
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1 M sodium citrate, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→31.35 Å / Num. obs: 41892 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
Aimlessccp4-6.5data scaling
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UL1

3ul1


Resolution: 2.1→31.35 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 2088 4.99 %Random selection
Rwork0.1825 ---
obs0.1838 41840 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→31.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 0 342 3713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013431
X-RAY DIFFRACTIONf_angle_d1.3394668
X-RAY DIFFRACTIONf_dihedral_angle_d13.9411263
X-RAY DIFFRACTIONf_chiral_restr0.064558
X-RAY DIFFRACTIONf_plane_restr0.008598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14890.28971110.2692657X-RAY DIFFRACTION100
2.1489-2.20260.28841370.25512673X-RAY DIFFRACTION100
2.2026-2.26210.31331470.2382623X-RAY DIFFRACTION100
2.2621-2.32870.23271540.21942631X-RAY DIFFRACTION100
2.3287-2.40380.2431280.21392644X-RAY DIFFRACTION100
2.4038-2.48970.25381270.20232660X-RAY DIFFRACTION100
2.4897-2.58930.20281360.2012636X-RAY DIFFRACTION99
2.5893-2.70710.26071320.19942659X-RAY DIFFRACTION99
2.7071-2.84980.24211480.19192640X-RAY DIFFRACTION99
2.8498-3.02820.1911310.19782647X-RAY DIFFRACTION99
3.0282-3.26170.22791440.19242637X-RAY DIFFRACTION99
3.2617-3.58960.18311370.1782658X-RAY DIFFRACTION98
3.5896-4.1080.16781390.15172652X-RAY DIFFRACTION98
4.108-5.17190.161620.14032632X-RAY DIFFRACTION97
5.1719-31.35830.20051550.16182703X-RAY DIFFRACTION95

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