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- PDB-7rg6: Importin alpha2 in complex with ORF4B Bat coronavirus HKU5 -

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Basic information

Entry
Database: PDB / ID: 7rg6
TitleImportin alpha2 in complex with ORF4B Bat coronavirus HKU5
Components
  • Importin subunit alpha-1
  • Non-structural protein ORF4b
KeywordsTRANSPORT PROTEIN / complex / transportin / importin / virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / 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 / host cell nucleolus / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / 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 / host cell nucleolus / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / host cell cytoplasm / postsynaptic density / glutamatergic synapse / host cell nucleus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Non-structural protein 3c, bat coronavirus HKU5 / 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 ...Non-structural protein 3c, bat coronavirus HKU5 / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Non-structural protein ORF4b / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bat coronavirus HKU5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFoster, J.K. / Tsimbalyuk, S. / Roby, J.A. / Aragao, D. / Forwood, J.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2003636 Australia
CitationJournal: Nat Commun / Year: 2022
Title: MERS-CoV ORF4b employs an unusual binding mechanism to target IMP alpha and block innate immunity.
Authors: Munasinghe, T.S. / Edwards, M.R. / Tsimbalyuk, S. / Vogel, O.A. / Smith, K.M. / Stewart, M. / Foster, J.K. / Bosence, L.A. / Aragao, D. / Roby, J.A. / Basler, C.F. / Forwood, J.K.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: 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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-1
C: Non-structural protein ORF4b
D: Non-structural protein ORF4b


Theoretical massNumber of molelcules
Total (without water)60,6953
Polymers60,6953
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.692, 90.310, 100.000
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-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) / References: UniProt: P52293
#2: Protein/peptide Non-structural protein ORF4b / ORF4b


Mass: 2713.272 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus HKU5 / Gene: ORF4b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3EXD3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH6.5, 0.6M Citrate, 0.01M DTT

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→29.99 Å / Num. obs: 42118 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 37.19 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.059 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4172 / Rpim(I) all: 0.831

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Processing

Software
NameVersionClassification
Coot1.19rc4_4035model building
PHENIX1.19rc4_4035refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVT

6bvt


Resolution: 2.1→29.66 Å / SU ML: 0.263 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 2085 4.96 %
Rwork0.205 39958 -
obs0.2058 42043 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 0 188 3549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183418
X-RAY DIFFRACTIONf_angle_d0.48014645
X-RAY DIFFRACTIONf_chiral_restr0.0352556
X-RAY DIFFRACTIONf_plane_restr0.0036594
X-RAY DIFFRACTIONf_dihedral_angle_d12.5521265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.36861570.31172577X-RAY DIFFRACTION98.84
2.15-2.20.32951340.29892644X-RAY DIFFRACTION99.36
2.2-2.260.29311410.26692631X-RAY DIFFRACTION99.57
2.26-2.330.27021560.25072608X-RAY DIFFRACTION99.64
2.33-2.40.27641370.25132646X-RAY DIFFRACTION99.82
2.4-2.490.27091350.24332637X-RAY DIFFRACTION99.43
2.49-2.590.26721440.23442632X-RAY DIFFRACTION99.28
2.59-2.710.27691360.22972646X-RAY DIFFRACTION99.78
2.71-2.850.20081210.21092669X-RAY DIFFRACTION99.79
2.85-3.030.23771390.21222672X-RAY DIFFRACTION99.86
3.03-3.260.23471230.21482677X-RAY DIFFRACTION99.43
3.26-3.590.22271470.20412664X-RAY DIFFRACTION99.4
3.59-4.110.19361490.17172684X-RAY DIFFRACTION99.47
4.11-5.170.17091480.16182720X-RAY DIFFRACTION99.58
5.17-29.660.1881180.19012851X-RAY DIFFRACTION98.64

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