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- PDB-4rxh: Crystal Structure of Importin-alpha from Neurospora crassa comple... -

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Basic information

Entry
Database: PDB / ID: 4rxh
TitleCrystal Structure of Importin-alpha from Neurospora crassa complexed with SV40NLS
Components
  • Importin subunit alpha
  • Large T antigen
KeywordsTRANSPORT PROTEIN / ARM repeat / NLS / nuclear import / importin-alpha
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / nuclear import signal receptor activity / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / nuclear import signal receptor activity / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / protein import into nucleus / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus ...Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / 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. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Large T antigen / Importin subunit alpha
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
Simian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7553 Å
AuthorsBernardes, N.E. / Takeda, A.A.S. / Fontes, M.R.M.
CitationJournal: Plos One / Year: 2015
Title: Structure of Importin-alpha from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal.
Authors: Bernardes, N.E. / Takeda, A.A. / Dreyer, T.R. / Freitas, F.Z. / Bertolini, M.C. / Fontes, M.R.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha
A: Large T antigen
C: Large T antigen


Theoretical massNumber of molelcules
Total (without water)55,5733
Polymers55,5733
Non-polymers00
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.127, 64.494, 185.650
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


Mass: 53602.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Strain: FGSC 9718 / Gene: 3H10.030 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9C2K9
#2: Protein/peptide Large T antigen / LT / LT-AG


Mass: 985.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Large T-antigen nuclear localization sequence / Source: (synth.) Simian virus 40
References: UniProt: P03070, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 Mm Bicine pH 8.5, 20%(w/v) PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→36.98 Å / Num. all: 55181 / Num. obs: 54993 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.75→1.82 Å / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UL1

3ul1


Resolution: 1.7553→36.975 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 1997 3.64 %RANDOM
Rwork0.183 ---
all0.184 54927 --
obs0.184 54927 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7553→36.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 0 349 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073332
X-RAY DIFFRACTIONf_angle_d1.0984527
X-RAY DIFFRACTIONf_dihedral_angle_d11.8371225
X-RAY DIFFRACTIONf_chiral_restr0.039544
X-RAY DIFFRACTIONf_plane_restr0.006574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7553-1.79910.30871330.29633529X-RAY DIFFRACTION94
1.7991-1.84780.29951390.25893701X-RAY DIFFRACTION99
1.8478-1.90220.25031400.22883735X-RAY DIFFRACTION100
1.9022-1.96360.25641420.21263762X-RAY DIFFRACTION100
1.9636-2.03370.23181410.19473722X-RAY DIFFRACTION100
2.0337-2.11510.21841420.18833754X-RAY DIFFRACTION100
2.1151-2.21140.21641420.18023754X-RAY DIFFRACTION100
2.2114-2.3280.20021420.18223779X-RAY DIFFRACTION100
2.328-2.47380.20541440.18383786X-RAY DIFFRACTION100
2.4738-2.66480.22921420.18853803X-RAY DIFFRACTION100
2.6648-2.93280.22121450.19673819X-RAY DIFFRACTION100
2.9328-3.3570.22621440.1963830X-RAY DIFFRACTION100
3.357-4.22840.1861470.16763880X-RAY DIFFRACTION100
4.2284-36.98270.19311540.16034076X-RAY DIFFRACTION100

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