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- PDB-9pyr: Importin alpha 2 in complex with Haliotid herpesvirus 1 large teg... -

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Basic information

Entry
Database: PDB / ID: 9pyr
TitleImportin alpha 2 in complex with Haliotid herpesvirus 1 large tegument protein NLS region
Components
  • GLU-THR-LYS-LYS-ARG-ARG-ARG-ILE
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Importin alpha 1 / Karyopherin subunit alpha-2 / haliotid herpesvirus 1 large tegument protein / UL36h
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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Haliotid herpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNath, B.K. / Swarbrick, C.M.D. / Forwood, J.K. / Sarker, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Viruses / Year: 2025
Title: Structural Insights into the Nuclear Import of Haliotid Herpesvirus 1 Large Tegument Protein Homologue.
Authors: Nath, B.K. / Swarbrick, C.M.D. / Schwab, R.H.M. / Ariawan, D. / Tietz, O. / Forwood, J.K. / Sarker, S.
History
DepositionAug 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: GLU-THR-LYS-LYS-ARG-ARG-ARG-ILE
E: Importin subunit alpha-1
M: GLU-THR-LYS-LYS-ARG-ARG-ARG-ILE


Theoretical massNumber of molelcules
Total (without water)57,9363
Polymers57,9363
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.537, 90.847, 100.948
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/peptide GLU-THR-LYS-LYS-ARG-ARG-ARG-ILE


Mass: 1333.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Haliotid herpesvirus 1
#2: 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 (E. coli) / References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.6M sodium citrate, 0.1M HEPES pH 7.0, and 10mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.6→29.71 Å / Num. obs: 22759 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 51.84 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 11.2
Reflection shellResolution: 2.6→2.71 Å / Num. unique obs: 15183 / Rpim(I) all: 0.328

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
Aimless0.7.13data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.71 Å / SU ML: 0.3187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2171 2023 4.76 %
Rwork0.1803 40453 -
obs0.182 22713 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.11 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 0 14 3391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643433
X-RAY DIFFRACTIONf_angle_d0.84834665
X-RAY DIFFRACTIONf_chiral_restr0.0431561
X-RAY DIFFRACTIONf_plane_restr0.0064595
X-RAY DIFFRACTIONf_dihedral_angle_d16.37561271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.32151400.28892967X-RAY DIFFRACTION99.62
2.67-2.740.29281410.25362860X-RAY DIFFRACTION99.47
2.74-2.820.28961510.23312868X-RAY DIFFRACTION99.41
2.82-2.910.2491550.22562910X-RAY DIFFRACTION99.45
2.91-3.010.26571380.22452944X-RAY DIFFRACTION99.58
3.01-3.130.28141580.22382875X-RAY DIFFRACTION99.51
3.13-3.270.22431360.20742899X-RAY DIFFRACTION99.31
3.28-3.450.25141350.19432865X-RAY DIFFRACTION98.94
3.45-3.660.24811320.17952940X-RAY DIFFRACTION99.1
3.66-3.940.21331390.16942885X-RAY DIFFRACTION99.18
3.95-4.340.17921600.15012892X-RAY DIFFRACTION99.12
4.34-4.970.17731410.14982847X-RAY DIFFRACTION98.52
4.97-6.250.22051590.182841X-RAY DIFFRACTION97.85
6.25-29.710.16711380.14482860X-RAY DIFFRACTION97.37

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