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- PDB-6bwb: Hendra virus W protein C-terminus in complex with Importin alpha ... -

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Basic information

Entry
Database: PDB / ID: 6bwb
TitleHendra virus W protein C-terminus in complex with Importin alpha 3 crystal form 3
Components
  • Importin subunit alpha-3
  • Protein W
KeywordsTRANSPORT PROTEIN / Complex / Hendra virus / Importin / Karyopherin / phosphoprotein / W
Function / homology
Function and homology information


response to leptomycin B / dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / nuclear pore / male germ cell nucleus / response to hydrogen peroxide ...response to leptomycin B / dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / nuclear pore / male germ cell nucleus / response to hydrogen peroxide / ISG15 antiviral mechanism / protein import into nucleus / nuclear membrane / gene expression / amyloid fibril formation / host cell nucleus / nucleoplasm / nucleus / cytoplasm / 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
Importin subunit alpha-3 / Protein W
Similarity search - Component
Biological speciesHomo sapiens (human)
Hendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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
A: Importin subunit alpha-3
B: Protein W


Theoretical massNumber of molelcules
Total (without water)55,0422
Polymers55,0422
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-10 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.160, 58.990, 169.289
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 Importin subunit alpha-3 / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


Mass: 50325.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00629
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium chloride, 0.1M MES pH6.5, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→29.495 Å / Num. obs: 22252 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rpim(I) all: 0.032 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 8.8 / Num. unique obs: 2139 / CC1/2: 0.973 / Rpim(I) all: 0.077 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.3→29.495 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.11
RfactorNum. reflection% reflection
Rfree0.2184 1119 5.04 %
Rwork0.1777 --
obs0.1798 22194 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 0 205 3624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063483
X-RAY DIFFRACTIONf_angle_d0.714754
X-RAY DIFFRACTIONf_dihedral_angle_d21.4781281
X-RAY DIFFRACTIONf_chiral_restr0.043571
X-RAY DIFFRACTIONf_plane_restr0.006618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40460.25631500.19142566X-RAY DIFFRACTION100
2.4046-2.53140.23441210.19642597X-RAY DIFFRACTION100
2.5314-2.68990.25691460.19222599X-RAY DIFFRACTION100
2.6899-2.89740.23581350.18522583X-RAY DIFFRACTION100
2.8974-3.18860.25091560.18942606X-RAY DIFFRACTION100
3.1886-3.64930.21211260.18742664X-RAY DIFFRACTION100
3.6493-4.59490.18661300.15262660X-RAY DIFFRACTION100
4.5949-29.49740.18431550.16682800X-RAY DIFFRACTION100

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