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- PDB-1y2a: Structure of mammalian importin bound to the non-classical PLSCR1-NLS -

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Basic information

Entry
Database: PDB / ID: 1y2a
TitleStructure of mammalian importin bound to the non-classical PLSCR1-NLS
Components
  • Importin alpha-2 SubunitImportin α
  • decamer fragment of Phospholipid scramblase 1
KeywordsPROTEIN TRANSPORT / Armadillo repeat / protein:peptide complex / superhelix of helices
Function / homology
Function and homology information


phosphatidylserine biosynthetic process / lead ion binding / positive regulation of chromosome separation / regulation of mast cell activation / regulation of Fc receptor mediated stimulatory signaling pathway / phosphatidylserine exposure on apoptotic cell surface / response to interferon-beta / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / phospholipid scramblase activity / mercury ion binding ...phosphatidylserine biosynthetic process / lead ion binding / positive regulation of chromosome separation / regulation of mast cell activation / regulation of Fc receptor mediated stimulatory signaling pathway / phosphatidylserine exposure on apoptotic cell surface / response to interferon-beta / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / phospholipid scramblase activity / mercury ion binding / plasma membrane phospholipid scrambling / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / nuclease activity / NLS-dependent protein nuclear import complex / CD4 receptor binding / postsynapse to nucleus signaling pathway / positive regulation of innate immune response / host cell / negative regulation of phagocytosis / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / epidermal growth factor receptor binding / negative regulation of viral genome replication / plasma membrane => GO:0005886 / acute-phase response / response to lead ion / platelet activation / SH3 domain binding / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / virus receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / collagen-containing extracellular matrix / defense response to virus / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / Hydrolases; Acting on ester bonds / membrane raft / glutamatergic synapse / apoptotic process / calcium ion binding / positive regulation of gene expression / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / magnesium ion binding / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Scramblase / Scramblase / 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. ...Scramblase / Scramblase / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Phospholipid scramblase 1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, M.-H. / Ben-Efraim, I. / Mitrousis, G. / Walker-Kopp, N. / Sims, P.J. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Phospholipid Scramblase 1 Contains a Nonclassical Nuclear Localization Signal with Unique Binding Site in Importin alpha
Authors: Chen, M.-H. / Ben-Efraim, I. / Mitrousis, G. / Walker-Kopp, N. / Sims, P.J. / Cingolani, G.
History
DepositionNov 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Importin alpha-2 Subunit
P: decamer fragment of Phospholipid scramblase 1


Theoretical massNumber of molelcules
Total (without water)47,5152
Polymers47,5152
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-2 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.239, 91.10, 97.247
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Importin alpha-2 Subunit / Importin α / Karyopherin alpha-2 subunit / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex ...Karyopherin alpha-2 subunit / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / Importin alpha P1


Mass: 46386.055 Da / Num. of mol.: 1 / Fragment: residues 70-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P52293
#2: Protein/peptide decamer fragment of Phospholipid scramblase 1 / PL scramblase 1 / Ca2+ / -dependent phospholipid scramblase 1 / Erythrocyte phospholipid scramblase / MmTRA1b


Mass: 1129.332 Da / Num. of mol.: 1 / Fragment: NLS / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens, gene PLSCR1
References: UniProt: O15162
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.358 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.6-0.7 M sodium citrate, 100 mM Hepes pH 6.0, 10 mM -mercaptoethonal, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: May 28, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 36323 / Num. obs: 33397 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.092 / Net I/σ(I): 18.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 775 / Rsym value: 0.25 / % possible all: 60.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3225 10 %RANDOM
Rwork0.229 ---
all0.2887 ---
obs0.2306 32164 --
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 0 134 3441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.2→2.21 Å
RfactorNum. reflection% reflection
Rfree0.337 42 -
Rwork0.279 --
obs-349 60.2 %

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