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- PDB-6bvt: Importin alpha 1 in cargo free state -

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Basic information

Entry
Database: PDB / ID: 6bvt
TitleImportin alpha 1 in cargo free state
ComponentsImportin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Importin / Karyopherin / Nuclear / Transport
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 / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSmith, K.M. / Tsimablyuk, S. / Edwards, M.R. / Aragao, D. / Cross, E.M. / Basler, C.F. / Forwood, J.K.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for importin alpha 3 specificity of W proteins in Hendra and Nipah viruses.
Authors: Smith, K.M. / Tsimbalyuk, S. / Edwards, M.R. / Cross, E.M. / Batra, J. / Soares da Costa, T.P. / Aragao, D. / Basler, C.F. / Forwood, J.K.
History
DepositionDec 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / 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 1.2Mar 29, 2023Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Assembly

Deposited unit
E: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)55,2681
Polymers55,2681
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.516, 90.007, 100.686
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) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.01M DTT, 0.1M sodium HEPES, 1M Ammonium Sulfate

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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 315r / Detector: CCD / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→24.54 Å / Num. obs: 24805 / % possible obs: 98.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.4 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.061 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2822 / CC1/2: 0.751 / Rpim(I) all: 0.365 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FC8

5fc8


Resolution: 2.5→24.54 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.79
RfactorNum. reflection% reflection
Rfree0.213 1262 5.09 %
Rwork0.1919 --
obs0.193 24772 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 0 117 3361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033302
X-RAY DIFFRACTIONf_angle_d0.5864500
X-RAY DIFFRACTIONf_dihedral_angle_d10.782004
X-RAY DIFFRACTIONf_chiral_restr0.039544
X-RAY DIFFRACTIONf_plane_restr0.004576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.2591550.22572618X-RAY DIFFRACTION100
2.6-2.71820.23721180.23062627X-RAY DIFFRACTION100
2.7182-2.86130.2441270.21422612X-RAY DIFFRACTION100
2.8613-3.04030.26521560.21332617X-RAY DIFFRACTION99
3.0403-3.27450.25961390.21562615X-RAY DIFFRACTION99
3.2745-3.60310.21581500.20092603X-RAY DIFFRACTION98
3.6031-4.12240.19971420.16582600X-RAY DIFFRACTION97
4.1224-5.18570.16551560.16182578X-RAY DIFFRACTION96
5.1857-24.540.19411190.18412640X-RAY DIFFRACTION93

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