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- PDB-7rg2: Importin alpha2 in complex with MERS ORF4B R33A mutant -

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Basic information

Entry
Database: PDB / ID: 7rg2
TitleImportin alpha2 in complex with MERS ORF4B R33A mutant
Components
  • Importin subunit alpha-1
  • ORF4b
KeywordsTRANSPORT PROTEIN/VIRAL PROTEIN / complex / transportin / importin / virus / 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 / 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


Theoretical massNumber of molelcules
Total (without water)57,8942
Polymers57,8942
Non-polymers00
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-2 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.850, 89.870, 100.460
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: R33A
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.: 276 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.7 M Sodium Citrate, 0.1 M HEPES pH 6.5

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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→29.96 Å / Num. obs: 48821 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 34.84 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.04 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / Num. unique obs: 3553 / 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→29.64 Å / SU ML: 0.2306 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 2440 5.01 %
Rwork0.1989 46311 -
obs0.1998 48751 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.17 Å2
Refinement stepCycle: LAST / Resolution: 2→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 276 3606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023387
X-RAY DIFFRACTIONf_angle_d0.49974608
X-RAY DIFFRACTIONf_chiral_restr0.0358556
X-RAY DIFFRACTIONf_plane_restr0.0034587
X-RAY DIFFRACTIONf_dihedral_angle_d13.47461242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.35571460.29652681X-RAY DIFFRACTION99.26
2.04-2.090.25611430.26482655X-RAY DIFFRACTION99.47
2.09-2.130.25321410.24912703X-RAY DIFFRACTION99.54
2.13-2.190.27761360.23062682X-RAY DIFFRACTION99.86
2.19-2.250.23331470.2212699X-RAY DIFFRACTION99.72
2.25-2.310.25811340.21242681X-RAY DIFFRACTION99.75
2.31-2.390.22851600.20772675X-RAY DIFFRACTION99.23
2.39-2.470.20091520.20372687X-RAY DIFFRACTION99.82
2.47-2.570.24281430.19752713X-RAY DIFFRACTION99.76
2.57-2.690.24491350.20922717X-RAY DIFFRACTION99.93
2.69-2.830.22531450.20412733X-RAY DIFFRACTION100
2.83-3.010.23181350.2152734X-RAY DIFFRACTION100
3.01-3.240.26081330.2072746X-RAY DIFFRACTION99.97
3.24-3.560.21941420.20562742X-RAY DIFFRACTION99.35
3.56-4.080.19251710.17572738X-RAY DIFFRACTION100
4.08-5.130.1821460.16062794X-RAY DIFFRACTION100
5.13-29.640.18381310.19852931X-RAY DIFFRACTION99.38

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