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- PDB-7n8j: Human importin alpha 1 in complex with Bimax2 peptide -

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Basic information

Entry
Database: PDB / ID: 7n8j
TitleHuman importin alpha 1 in complex with Bimax2 peptide
Components
  • BIMAX2
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / Karyopherin / importin / nuclear transport
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / regulation of DNA recombination / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear import signal receptor activity / nuclear localization sequence binding / CaMK IV-mediated phosphorylation of CREB ...Sensing of DNA Double Strand Breaks / regulation of DNA recombination / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear import signal receptor activity / nuclear localization sequence binding / CaMK IV-mediated phosphorylation of CREB / DNA metabolic process / NLS-bearing protein import into nucleus / positive regulation of type I interferon production / host cell / ISG15 antiviral mechanism / histone deacetylase binding / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / nuclear membrane / Estrogen-dependent gene expression / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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 speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDonnelly, C.M. / Cross, E.M. / Tsimbalyuk, S. / Forwood, J.K.
CitationJournal: To Be Published
Title: Human importin alpha 1:Bimax2 peptide complex
Authors: Donnelly, C.M. / Cross, E.M. / Tsimbalyuk, S. / Forwood, J.K.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: BIMAX2


Theoretical massNumber of molelcules
Total (without water)52,9272
Polymers52,9272
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.801, 84.706, 126.041
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 Importin subunit alpha-1 / / Karyopherin subunit alpha-2 / RAG cohort protein 1 / SRP1-alpha


Mass: 49205.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52292
#2: Protein/peptide BIMAX2


Mass: 3721.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 4 Å3/Da / Density % sol: 69.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.4 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→29.83 Å / Num. obs: 14410 / % possible obs: 99.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 68.63 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.287 / Rpim(I) all: 1.01 / Net I/σ(I): 6.3
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.312 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2590 / CC1/2: 0.684 / Rpim(I) all: 0.464 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKX

3ukx


Resolution: 3.2→29.83 Å / SU ML: 0.382 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 708 4.91 %
Rwork0.2267 13702 -
obs0.2276 14410 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.46 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 0 0 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323537
X-RAY DIFFRACTIONf_angle_d0.54894818
X-RAY DIFFRACTIONf_chiral_restr0.0349572
X-RAY DIFFRACTIONf_plane_restr0.0041621
X-RAY DIFFRACTIONf_dihedral_angle_d4.2533481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.35431470.30942673X-RAY DIFFRACTION99.82
3.45-3.790.29661280.24662709X-RAY DIFFRACTION99.65
3.79-4.340.22291410.21952727X-RAY DIFFRACTION100
4.34-5.460.19871520.19732732X-RAY DIFFRACTION100
5.46-29.830.23681400.21542861X-RAY DIFFRACTION99.27

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