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- PDB-8fuc: Crystal structure of mouse Importin alpha in complex with Hendra ... -

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Basic information

Entry
Database: PDB / ID: 8fuc
TitleCrystal structure of mouse Importin alpha in complex with Hendra virus matrix protein minor site NLS2
Components
  • Contaminant peptide KKLARE
  • Importin subunit alpha-1
  • Matrix protein
KeywordsTRANSPORT PROTEIN / Complex / importin / nuclear transport / viral protein
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 / virion assembly / virion component ...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 / virion assembly / virion component / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / host cell cytoplasm / structural constituent of virion / postsynaptic density / glutamatergic synapse / host cell nucleus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Viral matrix protein / 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 ...Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Viral matrix protein / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Matrix protein / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli BL21 (bacteria)
Hendra virus horse/Australia/Hendra/1994
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDonnelly, C.M. / Basler, C.F. / Scott, C. / Forwood, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI144880-02 United States
CitationJournal: Viruses / Year: 2023
Title: Henipavirus Matrix Protein Employs a Non-Classical Nuclear Localization Signal Binding Mechanism.
Authors: Donnelly, C.M. / Vogel, O.A. / Edwards, M.R. / Taylor, P.E. / Roby, J.A. / Forwood, J.K. / Basler, C.F.
History
DepositionJan 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein
B: Importin subunit alpha-1
F: Contaminant peptide KKLARE


Theoretical massNumber of molelcules
Total (without water)58,2563
Polymers58,2563
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.550, 90.180, 98.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein/peptide Matrix protein / Protein M


Mass: 2240.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hendra virus horse/Australia/Hendra/1994 / References: UniProt: O89341
#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(DE3) (bacteria) / References: UniProt: P52293
#3: Protein/peptide Contaminant peptide KKLARE


Mass: 746.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.98 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.72M sodium citrate, 0.1M sodium HEPES, 1% dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 12, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→29.62 Å / Num. obs: 41275 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 38.75 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.057 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3316 / CC1/2: 0.776 / Rpim(I) all: 0.302

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Processing

Software
NameVersionClassification
MOSFLM1.19.2_4158data reduction
Aimless1.19.2_4158data scaling
PHASERphasing
REFMAC1.19.2_4158refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.62 Å / SU ML: 0.2311 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 2037 4.94 %
Rwork0.1749 39171 -
obs0.177 41208 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 0 233 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393437
X-RAY DIFFRACTIONf_angle_d0.61794687
X-RAY DIFFRACTIONf_chiral_restr0.038567
X-RAY DIFFRACTIONf_plane_restr0.0045598
X-RAY DIFFRACTIONf_dihedral_angle_d4.3122472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.29671380.25912563X-RAY DIFFRACTION99.89
2.15-2.20.29391200.22652582X-RAY DIFFRACTION99.78
2.2-2.260.24781310.19962591X-RAY DIFFRACTION99.82
2.26-2.330.22961340.18872557X-RAY DIFFRACTION99.81
2.33-2.40.27461340.18832585X-RAY DIFFRACTION99.82
2.4-2.490.21261500.18222568X-RAY DIFFRACTION99.6
2.49-2.590.2571510.19972567X-RAY DIFFRACTION99.93
2.59-2.710.27561220.20142625X-RAY DIFFRACTION99.57
2.71-2.850.26971350.18292587X-RAY DIFFRACTION99.67
2.85-3.030.22491380.19892615X-RAY DIFFRACTION99.75
3.03-3.260.25271180.19782616X-RAY DIFFRACTION99.82
3.26-3.590.221210.17552649X-RAY DIFFRACTION100
3.59-4.110.17761620.15142621X-RAY DIFFRACTION99.78
4.11-5.170.17341320.13672666X-RAY DIFFRACTION99.71
5.17-29.620.19781510.16692779X-RAY DIFFRACTION99.59

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