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- PDB-8u36: The crystal structure of the classical binding interface of Impor... -

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Basic information

Entry
Database: PDB / ID: 8u36
TitleThe crystal structure of the classical binding interface of Importin alpha 2 and a nuclear localisation signal sequence in Frog siadenovirus core protein VII
Components
  • Importin subunit alpha-1
  • PVII
KeywordsVIRAL PROTEIN / Adenovirus protein VII / Nuclear localization / Importin alpha / DNA 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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus ...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 / cytoplasmic stress granule / protein import into nucleus / viral capsid / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol
Similarity search - Function
Adenoviral core protein VII / Adenoviral core protein VII / 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. ...Adenoviral core protein VII / Adenoviral core protein VII / 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 / PVII
Similarity search - Component
Biological speciesMus musculus (house mouse)
Frog siadenovirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAthukorala, A. / Donnelly, C.M. / Forwood, J.K. / Sarker, S.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To be published
Title: Structural and functional characterization of nuclear localization signals of pVII protein of Frog siadenovirus
Authors: Athukorala, A. / Donnelly, C.M. / Forwood, J.K. / Sarker, S.
History
DepositionSep 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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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: PVII
C: PVII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5955
Polymers57,5493
Non-polymers462
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-7 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.287, 89.291, 95.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 / Fragment: UNP residues 70-529
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 PVII


Mass: 1140.408 Da / Num. of mol.: 2 / Fragment: UNP residues 141-149 / Source method: obtained synthetically / Source: (synth.) Frog siadenovirus A / References: UniProt: Q9IIH8
#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


Mass: 18.015 Da / Num. of mol.: 56 / 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: 57.17 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.65 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
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→47.9 Å / Num. obs: 23326 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 49.41 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.8
Reflection shellResolution: 2.6→9.01 Å / Rmerge(I) obs: 1.925 / Num. unique obs: 2512 / Rpim(I) all: 0.871 / % possible all: 97.1

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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 7RG1

7rg1


Resolution: 2.6→47.9 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1122 4.82 %
Rwork0.2177 --
obs0.2188 23275 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 2 56 3351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133347
X-RAY DIFFRACTIONf_angle_d1.7754554
X-RAY DIFFRACTIONf_dihedral_angle_d17.3121223
X-RAY DIFFRACTIONf_chiral_restr0.088553
X-RAY DIFFRACTIONf_plane_restr0.042580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.610.36831650.3172620X-RAY DIFFRACTION96
2.61-2.750.33341550.29252657X-RAY DIFFRACTION97
2.75-2.920.2921330.27732702X-RAY DIFFRACTION98
2.92-3.150.33831030.26172798X-RAY DIFFRACTION100
3.15-3.470.26781520.24022774X-RAY DIFFRACTION100
3.47-3.970.24281100.19882835X-RAY DIFFRACTION100
3.97-50.18121780.17312783X-RAY DIFFRACTION100
5-47.90.21951260.20212984X-RAY DIFFRACTION100

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