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- PDB-6bvv: Nipah virus W protein C-terminus in complex with Importin alpha 3 -

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Basic information

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


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 ...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 / symbiont-mediated suppression of host innate immune response / 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)
Nipah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSmith, K.M. / Tsimbalyuk, S. / 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 13, 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)55,0992
Polymers55,0992
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-9 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.701, 65.610, 73.939
Angle α, β, γ (deg.)90.00, 99.79, 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: 4773.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Gene: P/V/C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0C1C7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium nitrate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→38.211 Å / Num. obs: 19881 / % possible obs: 98.9 % / Redundancy: 2.3 % / Rpim(I) all: 0.087 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1953 / Rpim(I) all: 0.274 / % possible all: 99.2

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.3→38.211 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.64
RfactorNum. reflection% reflection
Rfree0.2224 989 5 %
Rwork0.1994 --
obs0.2006 19788 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 192 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063464
X-RAY DIFFRACTIONf_angle_d0.7474728
X-RAY DIFFRACTIONf_dihedral_angle_d19.4021273
X-RAY DIFFRACTIONf_chiral_restr0.043567
X-RAY DIFFRACTIONf_plane_restr0.005616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.42130.27931400.21622681X-RAY DIFFRACTION99
2.4213-2.57290.26721470.21992669X-RAY DIFFRACTION99
2.5729-2.77160.27071390.23482677X-RAY DIFFRACTION98
2.7716-3.05040.24791490.21662677X-RAY DIFFRACTION99
3.0504-3.49150.24731360.21052698X-RAY DIFFRACTION98
3.4915-4.39790.19761340.1792686X-RAY DIFFRACTION98
4.3979-38.21650.16531440.17572711X-RAY DIFFRACTION97

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