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- PDB-5hhg: Mouse importin alpha: Dengue 2 NS5 C-terminal NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 5hhg
TitleMouse importin alpha: Dengue 2 NS5 C-terminal NLS peptide complex
Components
  • Importin subunit alpha-1
  • RNA-directed RNA polymerase NS5
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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity ...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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / nuclear membrane / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA-binding transcription factor binding / RNA helicase activity / postsynaptic density / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / glutamatergic synapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / nucleoplasm / ATP binding / membrane / metal ion 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 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Armadillo-like helical / Alpha Horseshoe / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Genome polyprotein / Importin subunit alpha-1
Similarity search - Component
Biological speciesDengue virus type 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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
DepositionJan 11, 2016Deposition 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 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RNA-directed RNA polymerase NS5
E: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)50,5972
Polymers50,5972
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-4 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.250, 88.960, 100.390
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 RNA-directed RNA polymerase NS5


Mass: 4324.827 Da / Num. of mol.: 1 / Fragment: UNP residues 3353-3388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969)
Strain: Puerto Rico/PR159-S1/1969 / Details (production host): PGEX4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12823, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#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: 46271.953 Da / Num. of mol.: 1 / Fragment: UNP residues 71-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52293
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5M Ammonium Sulfate, 0.1M Sodium HEPES

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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: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→31.32 Å / Num. obs: 36643 / % possible obs: 99.8 % / Redundancy: 4.4 % / Net I/σ(I): 23.5

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.2→31.32 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 1825 4.99 %
Rwork0.1762 --
obs0.1781 36589 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 0 311 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063433
X-RAY DIFFRACTIONf_angle_d0.9784671
X-RAY DIFFRACTIONf_dihedral_angle_d13.4981264
X-RAY DIFFRACTIONf_chiral_restr0.033558
X-RAY DIFFRACTIONf_plane_restr0.005599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25950.25951540.19292569X-RAY DIFFRACTION98
2.2595-2.3260.25581350.1892657X-RAY DIFFRACTION100
2.326-2.40110.25841360.18132640X-RAY DIFFRACTION100
2.4011-2.48680.2371360.17532651X-RAY DIFFRACTION100
2.4868-2.58640.19771480.17612623X-RAY DIFFRACTION100
2.5864-2.7040.23021230.17992676X-RAY DIFFRACTION100
2.704-2.84650.24851430.17522678X-RAY DIFFRACTION100
2.8465-3.02470.22961520.18522619X-RAY DIFFRACTION100
3.0247-3.2580.22971380.18822689X-RAY DIFFRACTION100
3.258-3.58540.22271370.18332708X-RAY DIFFRACTION100
3.5854-4.10330.1811280.15492709X-RAY DIFFRACTION100
4.1033-5.1660.21141520.15692721X-RAY DIFFRACTION100
5.166-31.32390.16981430.19092824X-RAY DIFFRACTION98

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