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- PDB-7rg0: Importin alpha2 in complex with MERS ORF4B R24A mutant -

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Basic information

Entry
Database: PDB / ID: 7rg0
TitleImportin alpha2 in complex with MERS ORF4B R24A mutant
Components
  • Importin subunit alpha-1
  • ORF4b
KeywordsTRANSPORT PROTEIN/Viral Protein / Complex / Transportin / Importin / Virus / TRANSPORT PROTEIN / TRANSPORT PROTEIN-Viral Protein complex
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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule ...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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / 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 1.0Jul 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-1
B: ORF4b


Theoretical massNumber of molelcules
Total (without water)57,8942
Polymers57,8942
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-3 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.731, 89.570, 99.840
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 ORF4b


Mass: 2625.196 Da / Num. of mol.: 1 / Mutation: R24A
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 / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.6 M Sodium Citrate, 0.1 M HEPES, pH 7.0

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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 EIGER2 X 16M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→29.89 Å / Num. obs: 52441 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 37.51 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3530 / Rpim(I) all: 0.5

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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→29.57 Å / SU ML: 0.2091 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 2416 5.03 %
Rwork0.195 45575 -
obs0.1958 47991 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.69 Å2
Refinement stepCycle: LAST / Resolution: 2→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 0 230 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023360
X-RAY DIFFRACTIONf_angle_d0.49644575
X-RAY DIFFRACTIONf_chiral_restr0.0357552
X-RAY DIFFRACTIONf_plane_restr0.0034583
X-RAY DIFFRACTIONf_dihedral_angle_d12.78931232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.2661280.27692449X-RAY DIFFRACTION91.84
2.04-2.090.31141510.25572578X-RAY DIFFRACTION96.5
2.09-2.130.29181360.24012661X-RAY DIFFRACTION99.25
2.13-2.190.24161470.2272643X-RAY DIFFRACTION99.79
2.19-2.250.24291170.21552684X-RAY DIFFRACTION99.82
2.25-2.310.23181620.20432645X-RAY DIFFRACTION99.89
2.31-2.390.25071490.20812684X-RAY DIFFRACTION99.93
2.39-2.470.25781380.20162652X-RAY DIFFRACTION99.96
2.47-2.570.21911400.1942667X-RAY DIFFRACTION99.93
2.57-2.690.20611430.21312709X-RAY DIFFRACTION100
2.69-2.830.23231290.20112710X-RAY DIFFRACTION100
2.83-3.010.22691510.21192683X-RAY DIFFRACTION99.96
3.01-3.240.23931410.21082706X-RAY DIFFRACTION99.86
3.24-3.560.23521420.20322726X-RAY DIFFRACTION100
3.56-4.080.18391470.17222739X-RAY DIFFRACTION100
4.08-5.130.18091590.16162742X-RAY DIFFRACTION100
5.13-29.570.18231360.18982897X-RAY DIFFRACTION99.41

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