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- PDB-6d7n: Crystal structure of the W357R/W399R Importin alpha mutant -

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Basic information

Entry
Database: PDB / ID: 6d7n
TitleCrystal structure of the W357R/W399R Importin alpha mutant
ComponentsPeroxidase,Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / IMPORTIN / NLS / BIPARTITE / PROTEIN BINDING
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 / peroxidase / lactoperoxidase activity / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / hydrogen peroxide catabolic process / cytoplasmic stress granule ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / peroxidase / lactoperoxidase activity / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / hydrogen peroxide catabolic process / cytoplasmic stress granule / protein import into nucleus / host cell / response to oxidative stress / DNA-binding transcription factor binding / postsynaptic density / heme binding / glutamatergic synapse / extracellular region / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Plant peroxidase / Secretory peroxidase / 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. ...Plant peroxidase / Secretory peroxidase / 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 / Peroxidases heam-ligand binding site / Armadillo/beta-catenin-like repeats / Armadillo / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Haem peroxidase superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Peroxidase / Importin subunit alpha-1
Similarity search - Component
Biological speciesPanicum virgatum (switchgrass)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPedersen, L.C. / London, R.E. / Gabel, S.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES050111 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES102645 United States
CitationJournal: Traffic / Year: 2018
Title: Variations in nuclear localization strategies among pol X family enzymes.
Authors: Kirby, T.W. / Pedersen, L.C. / Gabel, S.A. / Gassman, N.R. / London, R.E.
History
DepositionApr 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
B: Peroxidase,Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5836
Polymers55,2731
Non-polymers3105
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint12 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.402, 90.637, 100.831
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 Peroxidase,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: 55272.535 Da / Num. of mol.: 1 / Mutation: W357R, W399R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panicum virgatum (switchgrass), (gene. exp.) Mus musculus (house mouse)
Gene: PviPRX9, Kpna2, Rch1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1S4NYF8, UniProt: P52293, peroxidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.0M triammonium citrate, 0.1M Bis-Tris-Propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 28, 2018 / Details: VariMaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 32563 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.064 / Rrim(I) all: 0.164 / Net I/σ(I): 5.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1571 / CC1/2: 0.749 / Rpim(I) all: 0.395 / Rrim(I) all: 0.979 / Rsym value: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E6Q

5e6q


Resolution: 2.3→29.287 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2171 1621 4.99 %
Rwork0.1794 --
obs0.1813 32506 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 20 208 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113240
X-RAY DIFFRACTIONf_angle_d1.0474423
X-RAY DIFFRACTIONf_dihedral_angle_d10.561962
X-RAY DIFFRACTIONf_chiral_restr0.052544
X-RAY DIFFRACTIONf_plane_restr0.007569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.36790.30471290.23522483X-RAY DIFFRACTION99
2.3679-2.44430.34171250.24142573X-RAY DIFFRACTION100
2.4443-2.53160.26061360.22922511X-RAY DIFFRACTION100
2.5316-2.63290.30161350.23592544X-RAY DIFFRACTION100
2.6329-2.75270.27691320.21432551X-RAY DIFFRACTION100
2.7527-2.89770.23081400.20342556X-RAY DIFFRACTION100
2.8977-3.07910.25211350.21422557X-RAY DIFFRACTION100
3.0791-3.31650.22941350.192561X-RAY DIFFRACTION100
3.3165-3.64970.21371340.16162587X-RAY DIFFRACTION100
3.6497-4.17650.19021370.14722587X-RAY DIFFRACTION100
4.1765-5.2570.15861400.14252637X-RAY DIFFRACTION100
5.257-29.2890.18191430.16792738X-RAY DIFFRACTION100

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