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- PDB-6bw9: Hendra virus W protein C-terminus in complex with Importin alpha ... -

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Basic information

Entry
Database: PDB / ID: 6bw9
TitleHendra virus W protein C-terminus in complex with Importin alpha 3 crystal form 1
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 / ISG15 antiviral mechanism / protein import into nucleus ...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 / ISG15 antiviral mechanism / protein import into nucleus / gene expression / nuclear membrane / amyloid fibril formation / host cell nucleus / nucleoplasm / nucleus / cytosol / cytoplasm
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: 1.6 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

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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
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-11 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.430, 65.740, 74.190
Angle α, β, γ (deg.)90.00, 99.76, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 338 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium citrate pH 5.0, 20% w/v PEG 2000

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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: 1.6→19.84 Å / Num. obs: 58984 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.989 / Rpim(I) all: 0.061 / Net I/σ(I): 7.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2917 / CC1/2: 0.899 / Rpim(I) all: 0.174 / % possible all: 99.6

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.6→19.578 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.19
RfactorNum. reflection% reflection
Rfree0.1963 2894 4.91 %
Rwork0.1713 --
obs0.1725 58886 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 338 3738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153464
X-RAY DIFFRACTIONf_angle_d1.2164729
X-RAY DIFFRACTIONf_dihedral_angle_d19.8571272
X-RAY DIFFRACTIONf_chiral_restr0.069568
X-RAY DIFFRACTIONf_plane_restr0.009615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62620.23911340.20562666X-RAY DIFFRACTION99
1.6262-1.65420.24591280.1922645X-RAY DIFFRACTION99
1.6542-1.68430.25391440.19112660X-RAY DIFFRACTION99
1.6843-1.71670.21351620.17732604X-RAY DIFFRACTION99
1.7167-1.75170.19481330.17792652X-RAY DIFFRACTION99
1.7517-1.78980.2241210.17112650X-RAY DIFFRACTION100
1.7898-1.83140.20251440.17252716X-RAY DIFFRACTION99
1.8314-1.87710.17321510.17622604X-RAY DIFFRACTION100
1.8771-1.92790.21441280.17012706X-RAY DIFFRACTION100
1.9279-1.98450.20321390.16452675X-RAY DIFFRACTION100
1.9845-2.04850.20261290.16772669X-RAY DIFFRACTION100
2.0485-2.12160.16681220.16662683X-RAY DIFFRACTION100
2.1216-2.20650.20741530.16312678X-RAY DIFFRACTION100
2.2065-2.30680.19471450.16452672X-RAY DIFFRACTION100
2.3068-2.42820.19291490.16672648X-RAY DIFFRACTION100
2.4282-2.580.21441290.16752671X-RAY DIFFRACTION100
2.58-2.77870.20491430.1782703X-RAY DIFFRACTION100
2.7787-3.05740.20341260.17722667X-RAY DIFFRACTION99
3.0574-3.49760.16311390.17382712X-RAY DIFFRACTION100
3.4976-4.39830.18491220.15562709X-RAY DIFFRACTION99
4.3983-19.5790.18651530.17852602X-RAY DIFFRACTION95

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