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- PDB-3q5u: A minimal NLS from human scramblase 4 complexed with importin alpha -

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Basic information

Entry
Database: PDB / ID: 3q5u
TitleA minimal NLS from human scramblase 4 complexed with importin alpha
Components
  • Importin subunit alpha-2
  • Phospholipid scramblase 4
Keywordsprotein transport/membrane protein / Armadillo Repeat / Protein Transport / Protein transport-membrane protein complex
Function / homology
Function and homology information


phospholipid scramblase activity / Sensing of DNA Double Strand Breaks / plasma membrane phospholipid scrambling / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / CD4 receptor binding / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding ...phospholipid scramblase activity / Sensing of DNA Double Strand Breaks / plasma membrane phospholipid scrambling / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / CD4 receptor binding / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / SH3 domain binding / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / membrane => GO:0016020 / postsynaptic density / glutamatergic synapse / calcium ion binding / enzyme binding / nucleoplasm / nucleus / plasma membrane / cytosol
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
Importin subunit alpha-1 / Phospholipid scramblase 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBhardwaj, A. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: A Minimal Nuclear Localization Signal (NLS) in Human Phospholipid Scramblase 4 That Binds Only the Minor NLS-binding Site of Importin {alpha}1.
Authors: Lott, K. / Bhardwaj, A. / Sims, P.J. / Cingolani, G.
History
DepositionDec 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Aug 24, 2011Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.6Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-2
B: Phospholipid scramblase 4


Theoretical massNumber of molelcules
Total (without water)51,3722
Polymers51,3722
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.451, 90.973, 96.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer

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Components

#1: Protein Importin subunit alpha-2 / / 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: 49886.633 Da / Num. of mol.: 1 / Fragment: unp residues 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: PET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide Phospholipid scramblase 4 / / PL scramblase 4 / Ca(2+)-dependent phospholipid scramblase 4 / Cell growth-inhibiting gene 43 protein / TRA1


Mass: 1485.775 Da / Num. of mol.: 1 / Fragment: unp residues 271-283 / Source method: obtained synthetically
Details: human PLSCR4-NLS was synthesized by solid-phase methods and purified by reverse-phase HPLC (M.W. 1483.78 daltons)
References: UniProt: Q9NRQ2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3 uL of deltaIBB-importin alpha concentrated to 20 mg/ml were mixed with 0.7 microlitre of a 2-fold molar excess of hPLSCR4-NLS peptide; 3 uL of reservoir solution containing ~0.8 M sodium ...Details: 2.3 uL of deltaIBB-importin alpha concentrated to 20 mg/ml were mixed with 0.7 microlitre of a 2-fold molar excess of hPLSCR4-NLS peptide; 3 uL of reservoir solution containing ~0.8 M sodium citrate, 100 mM Hepes, and 10 mM beta-mercaptoethanol were added to the drop, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 10, 2010 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 22733 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.159 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.1 / % possible all: 67.3

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Processing

Software
NameVersionClassification
CrysalisProCCDdata collection
PHENIX(phenix.refine: 1.6.3_473)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1Y2A

1y2a


Resolution: 2.5→29.81 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.06 / Stereochemistry target values: ML
Details: Refinement using rigid body refinement, simulated annealing and isotropic B-factor in PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1127 5.05 %Random
Rwork0.1874 ---
obs0.1893 22316 91.87 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.45 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0993 Å2-0 Å20 Å2
2---2.187 Å2-0 Å2
3---0.0878 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 0 191 3485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083354
X-RAY DIFFRACTIONf_angle_d1.0924568
X-RAY DIFFRACTIONf_dihedral_angle_d15.2761227
X-RAY DIFFRACTIONf_chiral_restr0.083549
X-RAY DIFFRACTIONf_plane_restr0.004584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61370.3995980.30061749X-RAY DIFFRACTION62
2.6137-2.75140.28621230.25022268X-RAY DIFFRACTION80
2.7514-2.92370.27691390.21322712X-RAY DIFFRACTION96
2.9237-3.14920.2441510.19592806X-RAY DIFFRACTION98
3.1492-3.46570.24971520.19982824X-RAY DIFFRACTION99
3.4657-3.96620.20761450.16472896X-RAY DIFFRACTION100
3.9662-4.99310.16691590.14462898X-RAY DIFFRACTION100
4.9931-29.81220.19061600.17823036X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 75.8842 Å / Origin y: 68.7668 Å / Origin z: 48.735 Å
111213212223313233
T0.0076 Å20.0099 Å20.0271 Å2-0.03 Å2-0.0308 Å2--0.0106 Å2
L0.1898 °20.1489 °20.1221 °2-0.1363 °20.112 °2--0.1059 °2
S0.0208 Å °0.0797 Å °-0.0497 Å °0.0009 Å °0.0611 Å °-0.0351 Å °-0.0247 Å °0.0287 Å °0.1868 Å °
Refinement TLS groupSelection details: all

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