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- PDB-4htv: Mouse importin alpha: BFDV Cap NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 4htv
TitleMouse importin alpha: BFDV Cap NLS peptide complex
Components
  • Importin subunit alpha-2
  • capsid protein
KeywordsPROTEIN TRANSPORT/VIRAL PROTEIN / nuclear transporter / 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 / viral capsid assembly / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing 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 / viral capsid assembly / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / endocytosis involved in viral entry into host cell / cytoplasmic stress granule / viral penetration into host nucleus / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / host cell nucleus / virion attachment to host cell / nucleoplasm / nucleus / cytosol
Similarity search - Function
Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / 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. ...Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Putative capsid protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Beak and feather disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPatterson, E.I. / Forwood, J.K. / Raidal, S.R.
CitationJournal: TO BE PUBLISHED
Title: Mouse importin alpha: BFDV Cap NLS peptide complex
Authors: Patterson, E.I. / Forwood, J.K. / Raidal, S.R.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha-2
B: capsid protein


Theoretical massNumber of molelcules
Total (without water)59,5092
Polymers59,5092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint2 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.200, 89.900, 99.160
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-2 / 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: 55121.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-528
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
#2: Protein/peptide capsid protein


Mass: 4388.182 Da / Num. of mol.: 1 / Fragment: NLS peptide (UNP residues 11-39) / Source method: obtained synthetically / Source: (synth.) Beak and feather disease virus / References: UniProt: Q68SX0

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.675 M trisodium citrate, 20 mM DTT, 0.1 M HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 9, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→29.99 Å / Num. obs: 16074 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.153
Reflection shellResolution: 2.9→3.06 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
Cootmodel building
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→28.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.874 / SU B: 29.167 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 1.453 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22804 730 5 %RANDOM
Rwork0.17293 ---
all0.17558 16074 --
obs0.17558 13768 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 3→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 0 0 3332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9684615
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65925.29138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.05815590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8481516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 38 -
Rwork0.313 895 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 1.4361 Å / Origin y: 23.6067 Å / Origin z: -0.4323 Å
111213212223313233
T0.0193 Å2-0.0086 Å20.0055 Å2-0.0137 Å20.0103 Å2--0.0203 Å2
L0.5877 °2-0.53 °20.3718 °2-0.6507 °2-0.4353 °2--0.4141 °2
S0.0198 Å °-0.0831 Å °-0.0929 Å °0.0208 Å °0.0656 Å °0.0872 Å °-0.0456 Å °-0.034 Å °-0.0855 Å °

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