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- PDB-7rg3: Importin alpha2 in complex with MERS ORF4B R37A mutant -

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Basic information

Entry
Database: PDB / ID: 7rg3
TitleImportin alpha2 in complex with MERS ORF4B R37A mutant
Components
  • Importin subunit alpha-1
  • ORF4b
KeywordsTRANSPORT PROTEIN / complex / transportin / importin / virus
Function / homology
Function and homology information


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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha-1 / ORF4b
Similarity search - Component
Biological speciesMus musculus (house mouse)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.0Aug 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
B: ORF4b
C: ORF4b


Theoretical massNumber of molelcules
Total (without water)60,5193
Polymers60,5193
Non-polymers00
Water5,765320
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)78.731, 89.960, 100.549
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 (bacteria) / References: UniProt: P52293
#2: Protein/peptide ORF4b


Mass: 2625.196 Da / Num. of mol.: 2 / Mutation: R37A
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.7 M Sodium Citrate, 0.1 M HEPES, pH 7.5

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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: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→29.99 Å / Num. obs: 48968 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.37 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.038 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3566 / Rpim(I) all: 0.35

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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→29.62 Å / SU ML: 0.2103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1942 2442 4.99 %
Rwork0.1767 46450 -
obs0.1775 48892 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.09 Å2
Refinement stepCycle: LAST / Resolution: 2→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 320 3669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283407
X-RAY DIFFRACTIONf_angle_d0.55784635
X-RAY DIFFRACTIONf_chiral_restr0.0372558
X-RAY DIFFRACTIONf_plane_restr0.0042591
X-RAY DIFFRACTIONf_dihedral_angle_d14.10131253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.3211390.25662684X-RAY DIFFRACTION100
2.04-2.090.22891450.23192686X-RAY DIFFRACTION100
2.09-2.130.24351450.21412713X-RAY DIFFRACTION99.97
2.13-2.190.22481330.20162691X-RAY DIFFRACTION100
2.19-2.250.19141470.18742699X-RAY DIFFRACTION100
2.25-2.310.20871310.17412710X-RAY DIFFRACTION99.96
2.31-2.390.21231690.17582690X-RAY DIFFRACTION100
2.39-2.470.18151470.17272684X-RAY DIFFRACTION100
2.47-2.570.18351470.17492715X-RAY DIFFRACTION99.97
2.57-2.690.22761390.18862728X-RAY DIFFRACTION100
2.69-2.830.2051430.17762734X-RAY DIFFRACTION100
2.83-3.010.2081340.18862742X-RAY DIFFRACTION100
3.01-3.240.22621340.19592741X-RAY DIFFRACTION100
3.24-3.560.20291430.18322760X-RAY DIFFRACTION100
3.56-4.080.17651690.15562733X-RAY DIFFRACTION100
4.08-5.130.15661470.14012799X-RAY DIFFRACTION100
5.13-29.620.17361300.18072941X-RAY DIFFRACTION99.71

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