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- PDB-8fzm: Human importin alpha 3 in complex with Bimax2 peptide -

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Basic information

Entry
Database: PDB / ID: 8fzm
TitleHuman importin alpha 3 in complex with Bimax2 peptide
Components
  • Bimax2
  • Importin subunit alpha-3
KeywordsTRANSPORT PROTEIN / importin / nuclear transport / inhibitor
Function / homology
Function and homology information


dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear pore / ISG15 antiviral mechanism / protein import into nucleus / gene expression ...dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear pore / ISG15 antiviral mechanism / protein import into nucleus / gene expression / nuclear membrane / nucleoplasm / nucleus / 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-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDonnelly, C.M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human importin alpha 3 in complex with Bimax2 peptide
Authors: Donnelly, C.M. / Forwood, J.K.
History
DepositionJan 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-3
B: Bimax2
C: Importin subunit alpha-3
D: Bimax2


Theoretical massNumber of molelcules
Total (without water)107,9804
Polymers107,9804
Non-polymers00
Water00
1
A: Importin subunit alpha-3
B: Bimax2


Theoretical massNumber of molelcules
Total (without water)53,9902
Polymers53,9902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-1 kcal/mol
Surface area17920 Å2
MethodPISA
2
C: Importin subunit alpha-3
D: Bimax2


Theoretical massNumber of molelcules
Total (without water)53,9902
Polymers53,9902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-1 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.209, 91.610, 99.219
Angle α, β, γ (deg.)79.330, 81.040, 89.960
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Importin subunit alpha-3 / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


Mass: 50325.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00629
#2: Protein/peptide Bimax2


Mass: 3664.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M sodium HEPES, 0.78M sodium citrate, 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: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→24.85 Å / Num. obs: 31010 / % possible obs: 94.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 45.98 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.133 / Net I/σ(I): 3.8
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4496 / CC1/2: 0.716 / Rpim(I) all: 0.535

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BWB

6bwb


Resolution: 3→24.85 Å / SU ML: 0.399 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.2956 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 1543 4.98 %
Rwork0.2297 29427 -
obs0.2312 30970 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.61 Å2
Refinement stepCycle: LAST / Resolution: 3→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 0 0 6236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00926350
X-RAY DIFFRACTIONf_angle_d1.29218718
X-RAY DIFFRACTIONf_chiral_restr0.06761088
X-RAY DIFFRACTIONf_plane_restr0.01161132
X-RAY DIFFRACTIONf_dihedral_angle_d6.3333836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.37341320.36522620X-RAY DIFFRACTION93.35
3.1-3.210.30231450.28142700X-RAY DIFFRACTION94.11
3.21-3.340.2851470.26922665X-RAY DIFFRACTION93.89
3.34-3.490.33251200.25662710X-RAY DIFFRACTION94.55
3.49-3.670.29771350.23982686X-RAY DIFFRACTION94.47
3.67-3.90.22881390.22032624X-RAY DIFFRACTION93.16
3.9-4.20.26231310.20032635X-RAY DIFFRACTION92.6
4.2-4.620.20391510.18362683X-RAY DIFFRACTION94.62
4.62-5.280.21371330.2122771X-RAY DIFFRACTION95.97
5.28-6.630.29831580.24542668X-RAY DIFFRACTION95.31
6.63-24.850.22831520.20072665X-RAY DIFFRACTION93.59

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