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- PDB-8fub: Crystal structure of human Importin alpha 3 in complex with Hendr... -

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Basic information

Entry
Database: PDB / ID: 8fub
TitleCrystal structure of human Importin alpha 3 in complex with Hendra virus matrix protein NLS1
Components
  • Importin subunit alpha-3
  • Matrix protein
KeywordsTRANSPORT PROTEIN / Importin / nuclear transport
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 / virion assembly / nuclear pore / male germ cell nucleus / response to hydrogen peroxide ...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 / virion assembly / nuclear pore / male germ cell nucleus / response to hydrogen peroxide / virion component / ISG15 antiviral mechanism / protein import into nucleus / nuclear membrane / gene expression / structural constituent of virion / host cell cytoplasm / host cell nucleus / nucleoplasm / nucleus / cytosol / cytoplasm
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 / 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 / Matrix protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hendra virus horse/Australia/Hendra/1994
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 15, 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-3
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)52,4622
Polymers52,4622
Non-polymers00
Water00
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)49.060, 64.270, 158.580
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-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) / References: UniProt: O00629
#2: Protein/peptide Matrix protein / Protein M


Mass: 2136.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hendra virus horse/Australia/Hendra/1994 / References: UniProt: O89341

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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: 2.5 Å3/Da / Density % sol: 50.83 %
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 EIGER2 S 16M / Detector: PIXEL / Date: Jul 25, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→29.78 Å / Num. obs: 13681 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 65.77 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.181 / Net I/σ(I): 7.8
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1966 / CC1/2: 0.887 / Rpim(I) all: 0.446

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MOSFLM1.14_3260data reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVZ

6bvz


Resolution: 2.75→29.78 Å / SU ML: 0.3291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2044 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2811 671 4.93 %
Rwork0.2411 12951 -
obs0.243 13622 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.53 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 0 0 3230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283286
X-RAY DIFFRACTIONf_angle_d0.57034486
X-RAY DIFFRACTIONf_chiral_restr0.0387548
X-RAY DIFFRACTIONf_plane_restr0.0041580
X-RAY DIFFRACTIONf_dihedral_angle_d15.64742006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.960.36581390.30542522X-RAY DIFFRACTION99.78
2.96-3.260.36211400.29122548X-RAY DIFFRACTION99.85
3.26-3.730.31051200.26822565X-RAY DIFFRACTION99.85
3.73-4.70.26781370.22672591X-RAY DIFFRACTION99.89
4.7-29.780.23921350.21572725X-RAY DIFFRACTION99.51

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