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- PDB-4b8o: rImp_alpha_SV40TAgNLS -

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Basic information

Entry
Database: PDB / ID: 4b8o
TitlerImp_alpha_SV40TAgNLS
Components
  • IMPORTIN SUBUNIT ALPHA-1A
  • SV40TAGNLS
KeywordsTRANSPORT PROTEIN / NUCLEAR LOCALIZATION SIGNAL
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / perinuclear region of cytoplasm / ATP binding / nucleus
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 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. ...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 / 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 / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / 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-1a
Similarity search - Component
Biological speciesORYZA SATIVA JAPONICA GROUP (Japanese rice)
SIMIAN VIRUS 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.084 Å
AuthorsChang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal Structure of Rice Importin-Alpha and Structural Basis of its Interaction with Plant-Specific Nuclear Localization Signals.
Authors: Chang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionAug 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMPORTIN SUBUNIT ALPHA-1A
B: SV40TAGNLS
C: SV40TAGNLS


Theoretical massNumber of molelcules
Total (without water)55,4003
Polymers55,4003
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-3.1 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.494, 73.865, 62.064
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21A-2006-

HOH

31A-2012-

HOH

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Components

#1: Protein IMPORTIN SUBUNIT ALPHA-1A /


Mass: 53026.848 Da / Num. of mol.: 1 / Fragment: NLS BINDING DOMAIN, RESIDUES 73-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA JAPONICA GROUP (Japanese rice)
Plasmid: PET30A_RIMPALPHA1A_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4
#2: Protein/peptide SV40TAGNLS


Mass: 1186.470 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SIMIAN VIRUS 40 / Plasmid: PGEX2T-SV40TAGNLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7XWN5*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.19 Å3/Da / Density % sol: 61.46 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M BIS-TRIS PROPANE PH 7.0, 14% PEG 3350, 0.2 M NDSB-221 (SIGMA) AND 0.2 M NAF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.08→64.62 Å / Num. obs: 35070 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.6 / % possible all: 82.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.084→46.145 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1755 5 %
Rwork0.167 --
obs0.1688 35053 96.92 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.221 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.9203 Å20 Å22.4858 Å2
2--12.8934 Å20 Å2
3----8.9731 Å2
Refinement stepCycle: LAST / Resolution: 2.084→46.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 201 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073392
X-RAY DIFFRACTIONf_angle_d0.9614607
X-RAY DIFFRACTIONf_dihedral_angle_d13.9181251
X-RAY DIFFRACTIONf_chiral_restr0.065552
X-RAY DIFFRACTIONf_plane_restr0.005591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.084-2.14030.2124810.19851929X-RAY DIFFRACTION72
2.1403-2.20330.21711290.17472470X-RAY DIFFRACTION95
2.2033-2.27440.18771190.17052596X-RAY DIFFRACTION99
2.2744-2.35570.24151250.17632621X-RAY DIFFRACTION99
2.3557-2.450.20681490.17442606X-RAY DIFFRACTION99
2.45-2.56150.21621350.17142600X-RAY DIFFRACTION99
2.5615-2.69660.23021380.17512640X-RAY DIFFRACTION100
2.6966-2.86550.19871540.17232579X-RAY DIFFRACTION99
2.8655-3.08670.19651550.17042622X-RAY DIFFRACTION99
3.0867-3.39720.2171400.1712616X-RAY DIFFRACTION100
3.3972-3.88860.17521490.15642658X-RAY DIFFRACTION100
3.8886-4.89830.18931380.14052644X-RAY DIFFRACTION100
4.8983-46.15650.20891430.18212717X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.0214 Å / Origin y: 0.2115 Å / Origin z: 6.5701 Å
111213212223313233
T0.1416 Å20.0041 Å2-0.0021 Å2-0.1058 Å2-0.0079 Å2--0.1502 Å2
L0.3552 °20.1604 °2-0.0874 °2-0.1634 °2-0.2194 °2--0.5102 °2
S0.0077 Å °-0.0285 Å °0.0147 Å °0.0055 Å °-0.0119 Å °-0.0222 Å °-0.0163 Å °-0.0376 Å °0.0033 Å °
Refinement TLS groupSelection details: ALL

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