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- PDB-8sv0: The crystal structure of the classical binding interface of Impor... -

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Basic information

Entry
Database: PDB / ID: 8sv0
TitleThe crystal structure of the classical binding interface of Importin alpha 2 and nuclear localisation signal sequence in Psittacine siadenovirus core protein VII
Components
  • Importin subunit alpha-1
  • protein VII
KeywordsPROTEIN TRANSPORT/VIRAL PROTEIN / Adenovirus protein VII / Nuclear localization / Importin alpha / DNA virus / PROTEIN TRANSPORT-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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Psittacine siadenovirus F
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAthukorala, A. / Sarker, S. / Forwood, J.K. / Donnelly, C.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other government Australia
CitationJournal: To Be Published
Title: Structural and functional characterization of nuclear localization signal of pVII protein of psittacine siadenovirus F demonstrates an independent transport of pVII protein into the nucleus
Authors: Athukorala, A. / Sarker, S. / Forwood, J.K. / Donnelly, C.M.
History
DepositionMay 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Importin subunit alpha-1
C: protein VII
E: protein VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4955
Polymers57,4493
Non-polymers462
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-18 kcal/mol
Surface area17800 Å2
Unit cell
Length a, b, c (Å)77.217, 88.728, 96.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 protein VII


Mass: 1090.326 Da / Num. of mol.: 2 / Fragment: nuclear localization signal / Source method: obtained synthetically / Source: (synth.) Psittacine siadenovirus F
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.6 M sodium citrate, 0.1 M sodium HEPES, 1% dithiothreitol

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Data collection

DiffractionMean temperature: 100 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: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→29.67 Å / Num. obs: 34168 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 47.44 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.075 / Net I/σ(I): 4
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.791 / Num. unique obs: 2903 / CC1/2: 0.319 / Rpim(I) all: 0.842 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UKX

3ukx


Resolution: 2.2→29.67 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1678 4.93 %
Rwork0.2294 --
obs0.2304 34056 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.82 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 2 76 3454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013444
X-RAY DIFFRACTIONf_angle_d1.4154683
X-RAY DIFFRACTIONf_dihedral_angle_d14.6291270
X-RAY DIFFRACTIONf_chiral_restr0.082560
X-RAY DIFFRACTIONf_plane_restr0.023599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.36141292605X-RAY DIFFRACTION98
2.26-2.340.36931600.39312631X-RAY DIFFRACTION99
2.34-2.420.36311350.34862652X-RAY DIFFRACTION99
2.42-2.520.33351180.30652675X-RAY DIFFRACTION99
2.52-2.630.31531310.29712683X-RAY DIFFRACTION100
2.63-2.770.29281330.27092706X-RAY DIFFRACTION100
2.77-2.940.29811480.28712662X-RAY DIFFRACTION100
2.95-3.170.30011660.26372704X-RAY DIFFRACTION100
3.17-3.490.2471500.25162691X-RAY DIFFRACTION100
3.49-3.990.22281310.20392729X-RAY DIFFRACTION99
4-5.030.19291440.17692760X-RAY DIFFRACTION100
5.03-29.670.18951330.19392880X-RAY DIFFRACTION99

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