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

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Basic information

Entry
Database: PDB / ID: 8fua
TitleCrystal structure of mouse Importin alpha in complex with Hendra virus matrix protein NLS1
Components
  • Importin subunit alpha-1
  • Matrix protein
KeywordsTRANSPORT PROTEIN / 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 / virion assembly / virion component / protein import into nucleus / 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 / virion assembly / virion component / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / structural constituent of virion / host cell cytoplasm / postsynaptic density / host cell nucleus / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
: / Paramyxoviridae matrix protein C-terminal domain / Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Paramyxoviridae matrix protein N-terminal domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...: / Paramyxoviridae matrix protein C-terminal domain / Viral matrix protein / Viral matrix protein, C-terminal domain / Viral matrix protein, N-terminal domain / Paramyxoviridae matrix protein N-terminal domain / 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)
Hendra virus horse/Australia/Hendra/1994
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 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: Importin subunit alpha-1
B: Matrix protein
C: Matrix protein


Theoretical massNumber of molelcules
Total (without water)59,5423
Polymers59,5423
Non-polymers00
Water4,558253
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)78.488, 89.859, 99.829
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 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
#2: Protein/peptide Matrix protein / Protein M


Mass: 2136.585 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus horse/Australia/Hendra/1994
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O89341
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.96 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M sodium HEPES, 0.72M sodium citrate, 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 EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→24.42 Å / Num. obs: 56224 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 35.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.05 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.376 / Num. unique obs: 26486 / CC1/2: 0.602 / Rpim(I) all: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BW0

6bw0


Resolution: 1.9→24.42 Å / SU ML: 0.2161 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.0206 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19 2864 5.09 %
Rwork0.1728 53360 -
obs0.1737 56224 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 0 253 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01473292
X-RAY DIFFRACTIONf_angle_d1.17814486
X-RAY DIFFRACTIONf_chiral_restr0.072551
X-RAY DIFFRACTIONf_plane_restr0.0096570
X-RAY DIFFRACTIONf_dihedral_angle_d15.44491990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.34921530.29612599X-RAY DIFFRACTION100
1.93-1.970.28941690.27582646X-RAY DIFFRACTION100
1.97-2.010.30591300.25352638X-RAY DIFFRACTION100
2.01-2.050.26381330.232642X-RAY DIFFRACTION99.93
2.05-2.090.22291450.21762619X-RAY DIFFRACTION99.93
2.09-2.140.22941330.20852656X-RAY DIFFRACTION99.96
2.14-2.190.2621410.20192659X-RAY DIFFRACTION100
2.19-2.250.21911370.17932640X-RAY DIFFRACTION100
2.25-2.320.20321300.17362661X-RAY DIFFRACTION99.86
2.32-2.390.21461480.17572650X-RAY DIFFRACTION99.96
2.39-2.480.24441290.17512635X-RAY DIFFRACTION99.78
2.48-2.580.22821400.17432659X-RAY DIFFRACTION99.79
2.58-2.70.19711390.18012652X-RAY DIFFRACTION99.71
2.7-2.840.19521460.17152663X-RAY DIFFRACTION99.82
2.84-3.010.19971460.1782673X-RAY DIFFRACTION99.93
3.01-3.250.20451650.17532655X-RAY DIFFRACTION100
3.25-3.570.17561400.16832707X-RAY DIFFRACTION100
3.57-4.090.14221470.14092705X-RAY DIFFRACTION100
4.09-5.140.1381380.13892751X-RAY DIFFRACTION100
5.14-24.420.18181550.18132850X-RAY DIFFRACTION99.6

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