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- PDB-7rfy: Importin alpha3 in complex with MERS ORF4B -

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Basic information

Entry
Database: PDB / ID: 7rfy
TitleImportin alpha3 in complex with MERS ORF4B
Components
  • Importin subunit alpha-3
  • ORF4b
KeywordsTRANSPORT PROTEIN/Viral Protein / Complex / Transportin / Importin / Virus / TRANSPORT PROTEIN / TRANSPORT PROTEIN-Viral Protein complex
Function / homology
Function and homology information


NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear pore / male germ cell nucleus / response to hydrogen peroxide / ISG15 antiviral mechanism / protein import into nucleus ...NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear pore / male germ cell nucleus / response to hydrogen peroxide / ISG15 antiviral mechanism / protein import into nucleus / nuclear membrane / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-3 / ORF4b
Similarity search - Component
Biological speciesHomo sapiens (human)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMunasinghe, T.S. / 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 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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-3
B: ORF4b


Theoretical massNumber of molelcules
Total (without water)53,0372
Polymers53,0372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.222, 59.711, 82.640
Angle α, β, γ (deg.)90.000, 98.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 ORF4b


Mass: 2711.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2BB21

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.0, 20% w/v PEG 6000

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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: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→25.99 Å / Num. obs: 15900 / % possible obs: 98.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 56.57 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1762 / Rsym value: 0.72

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Processing

Software
NameVersionClassification
autoBUSTER1.18.2_3874phasing
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVZ

6bvz


Resolution: 2.5→25.99 Å / SU ML: 0.3854 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.2881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2673 785 4.96 %
Rwork0.2487 15056 -
obs0.2497 15841 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.96 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 0 0 3143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033203
X-RAY DIFFRACTIONf_angle_d0.59514370
X-RAY DIFFRACTIONf_chiral_restr0.0441526
X-RAY DIFFRACTIONf_plane_restr0.0039563
X-RAY DIFFRACTIONf_dihedral_angle_d16.96421173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.47721280.42632473X-RAY DIFFRACTION96.94
2.66-2.860.35591260.35952490X-RAY DIFFRACTION97.21
2.86-3.150.3451490.30532468X-RAY DIFFRACTION98.01
3.15-3.60.30771160.25022518X-RAY DIFFRACTION97.59
3.6-4.540.22361200.20622547X-RAY DIFFRACTION98.02
4.54-25.990.22011460.21932560X-RAY DIFFRACTION97.72

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