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- PDB-6bw1: Hendra virus W protein C-terminus in complex with Importin alpha 1 -

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Basic information

Entry
Database: PDB / ID: 6bw1
TitleHendra virus W protein C-terminus in complex with Importin alpha 1
Components
  • Importin subunit alpha-1
  • Protein W
KeywordsTRANSPORT PROTEIN / Complex / Hendra virus / Importin / Karyopherin / phosphoprotein / W
Function / homology
Function and homology information


response to leptomycin B / 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 / protein import into nucleus / cytoplasmic stress granule / host cell ...response to leptomycin B / 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 / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / amyloid fibril formation / postsynaptic density / host cell nucleus / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / 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 ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein W / Importin subunit alpha-1
Similarity search - Component
Biological speciesHendra virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTsimbalyuk, S. / Smith, K.M. / Edwards, M.R. / Aragao, D. / Cross, E.M. / Basler, C.F. / Forwood, J.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for importin alpha 3 specificity of W proteins in Hendra and Nipah viruses.
Authors: Smith, K.M. / Tsimbalyuk, S. / Edwards, M.R. / Cross, E.M. / Batra, J. / Soares da Costa, T.P. / Aragao, D. / Basler, C.F. / Forwood, J.K.
History
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 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 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 29, 2023Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Protein W
E: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)59,9842
Polymers59,9842
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-3 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.040, 89.270, 100.430
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 Protein W


Mass: 4715.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus / Gene: P/V/C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0C1C6
#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) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.01M DTT, 0.1M sodium HEPES pH7, 0.7M sodium citrate

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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: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→19.76 Å / Num. obs: 36721 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 5.4 / Num. unique obs: 3139 / CC1/2: 0.928 / Rpim(I) all: 0.147 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.2→19.76 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6
RfactorNum. reflection% reflection
Rfree0.2122 1861 5.08 %
Rwork0.1915 --
obs0.1925 36662 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 125 3431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033365
X-RAY DIFFRACTIONf_angle_d0.6194583
X-RAY DIFFRACTIONf_dihedral_angle_d13.8761234
X-RAY DIFFRACTIONf_chiral_restr0.04554
X-RAY DIFFRACTIONf_plane_restr0.004585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25950.26951400.22922624X-RAY DIFFRACTION100
2.2595-2.32590.24151470.22012648X-RAY DIFFRACTION100
2.3259-2.40080.24441420.22092634X-RAY DIFFRACTION100
2.4008-2.48650.21711400.20992654X-RAY DIFFRACTION100
2.4865-2.58580.28671320.21662638X-RAY DIFFRACTION100
2.5858-2.70320.2261230.22522673X-RAY DIFFRACTION100
2.7032-2.84540.21621470.21272667X-RAY DIFFRACTION100
2.8454-3.02310.23721540.21862640X-RAY DIFFRACTION100
3.0231-3.25550.23671390.21192680X-RAY DIFFRACTION100
3.2555-3.58140.23671510.20142685X-RAY DIFFRACTION100
3.5814-4.09560.17931500.16592698X-RAY DIFFRACTION100
4.0956-5.14490.16041430.15442728X-RAY DIFFRACTION100
5.1449-19.76070.18981530.16252832X-RAY DIFFRACTION99

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