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- PDB-7rfz: Importin alpha 2 in complex with MERS ORF4B NLS peptide -

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Basic information

Entry
Database: PDB / ID: 7rfz
TitleImportin alpha 2 in complex with MERS ORF4B NLS peptide
Components
  • Importin subunit alpha-1
  • ORF4b
KeywordsTRANSPORT PROTEIN/Viral Protein / imortin / complex / nuclear import / 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 / protein import into nucleus / cytoplasmic stress granule / 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 / protein import into nucleus / cytoplasmic stress granule / 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: 1.95 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 1.1Aug 25, 2021Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Feb 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 1.3Oct 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)57,9802
Polymers57,9802
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint2 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.510, 89.530, 100.060
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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.65 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 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: 1.95→29.84 Å / Num. obs: 52136 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 34.65 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 2 / Num. unique obs: 3622 / Rsym value: 0.64

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Processing

Software
NameVersionClassification
PHASER1.19rc4_4035phasing
PHENIX1.19rc4_4035refinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVT

6bvt


Resolution: 1.95→29.51 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2114 2645 5.08 %
Rwork0.1881 49411 -
obs0.1893 52056 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.87 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 0 166 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263469
X-RAY DIFFRACTIONf_angle_d0.58764718
X-RAY DIFFRACTIONf_chiral_restr0.0382565
X-RAY DIFFRACTIONf_plane_restr0.0045602
X-RAY DIFFRACTIONf_dihedral_angle_d13.54721279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.33791380.30532576X-RAY DIFFRACTION99.96
1.99-2.020.3061470.29052540X-RAY DIFFRACTION100
2.02-2.060.28921290.25712573X-RAY DIFFRACTION100
2.06-2.110.27331330.24762558X-RAY DIFFRACTION99.96
2.11-2.160.27771340.2262582X-RAY DIFFRACTION100
2.16-2.210.26141150.21842575X-RAY DIFFRACTION100
2.21-2.270.23161260.19482606X-RAY DIFFRACTION99.96
2.27-2.340.21191490.18292556X-RAY DIFFRACTION100
2.34-2.410.2031480.19522574X-RAY DIFFRACTION100
2.41-2.50.23561350.18992604X-RAY DIFFRACTION99.93
2.5-2.60.22151570.19192534X-RAY DIFFRACTION100
2.6-2.720.26261240.20912640X-RAY DIFFRACTION100
2.72-2.860.24321520.19952560X-RAY DIFFRACTION100
2.86-3.040.24911400.20812618X-RAY DIFFRACTION100
3.04-3.280.25111250.21252620X-RAY DIFFRACTION100
3.28-3.610.22471330.19882641X-RAY DIFFRACTION100
3.61-4.130.18691650.15962613X-RAY DIFFRACTION100
4.13-5.190.15621340.14172673X-RAY DIFFRACTION100
5.19-29.510.15941610.16992768X-RAY DIFFRACTION99.66

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