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- PDB-3oqs: Crystal structure of importin-alpha bound to a CLIC4 NLS peptide -

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Basic information

Entry
Database: PDB / ID: 3oqs
TitleCrystal structure of importin-alpha bound to a CLIC4 NLS peptide
Components
  • Importin subunit alpha-2
  • peptide of Chloride intracellular channel protein 4
KeywordsPROTEIN TRANSPORT / importin alpha / karyopherin alpha / nuclear localisation signal (NLS) recognition / chloride intracellular channel 4 / CLIC4 NLS / Armadillo repeat / Nuclear import
Function / homology
Function and homology information


establishment or maintenance of apical/basal cell polarity / retina vasculature morphogenesis in camera-type eye / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / endothelial cell morphogenesis / positive regulation of viral life cycle / vacuolar acidification / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / fertilization ...establishment or maintenance of apical/basal cell polarity / retina vasculature morphogenesis in camera-type eye / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / endothelial cell morphogenesis / positive regulation of viral life cycle / vacuolar acidification / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / fertilization / host cell / chloride transport / nuclear import signal receptor activity / nuclear localization sequence binding / regulation of cytoskeleton organization / NLS-bearing protein import into nucleus / chloride channel activity / branching morphogenesis of an epithelial tube / microvillus / chloride channel complex / keratinocyte differentiation / cellular response to calcium ion / negative regulation of cell migration / multicellular organism growth / cytoplasmic vesicle membrane / nuclear matrix / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / cell-cell junction / actin cytoskeleton / apical part of cell / midbody / angiogenesis / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / cell differentiation / centrosome / glutamatergic synapse / perinuclear region of cytoplasm / cell surface / mitochondrion / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / 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. ...Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / 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 / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Armadillo-like helical / Alpha Horseshoe / Thioredoxin-like superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Chloride intracellular channel protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMynott, A.V. / Brown, L.J. / Harrop, S.J. / Curmi, P.M.G.
CitationJournal: Febs J. / Year: 2011
Title: Crystal structure of importin-alpha bound to a peptide bearing the nuclear localisation signal from chloride intracellular channel protein 4
Authors: Mynott, A.V. / Harrop, S.J. / Brown, L.J. / Breit, S.N. / Kobe, B. / Curmi, P.M.G.
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Assembly

Deposited unit
B: peptide of Chloride intracellular channel protein 4
A: Importin subunit alpha-2


Theoretical massNumber of molelcules
Total (without water)56,5392
Polymers56,5392
Non-polymers00
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-1 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.594, 89.558, 100.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide peptide of Chloride intracellular channel protein 4 / Intracellular chloride ion channel protein p64H1


Mass: 1208.495 Da / Num. of mol.: 1
Fragment: NLS (Nuclear Localisation Signal) UNP residues 198-207
Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y696
#2: Protein Importin subunit alpha-2 / / Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex ...Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / Importin alpha P1


Mass: 55330.566 Da / Num. of mol.: 1 / Fragment: NLS Binding Domain (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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 3.11 Å3/Da / Density % sol: 60.51 % / Mosaicity: 0.5 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.7M sodium citrate, 10mM DTT, 70mM HEPES pH 7.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→66.739 Å / Num. all: 46758 / Num. obs: 46758 / % possible obs: 96.7 % / Redundancy: 6.8 % / Rsym value: 0.096 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.114.90.8710.7760.72708055200.3810.8710.7761.880.3
2.11-2.246.20.6160.5641.23982864150.2410.6160.5642.997.5
2.24-2.397.20.4030.3731.64478162320.150.4030.3735.4100
2.39-2.587.30.250.2323.14250558020.0920.250.2327.3100
2.58-2.837.30.1740.1613.93936253640.0640.1740.16110.5100
2.83-3.167.30.1030.0967.13573448690.0380.1030.09615.3100
3.16-3.657.30.0750.0699.13131743110.0280.0750.06921.8100
3.65-4.477.20.0550.05111.22656837050.0210.0550.05129.5100
4.47-6.3270.0460.04312.92044229050.0170.0460.04328100
6.32-21.0516.50.0450.04110.71055116350.0180.0450.04130.897.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAL
Resolution: 2→21.05 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.1846 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8499 / SU R Cruickshank DPI: 0.143 / SU Rfree: 0.1406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. SOLVENT MOLECULES WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. SOLVENT MOLECULES WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 2366 5.1 %RANDOM
Rwork0.1969 ---
obs0.199 46695 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 106.38 Å2 / Biso mean: 36.2975 Å2 / Biso min: 10.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→21.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 0 356 3656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223387
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.974619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9685440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86825.672134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78515594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7751513
X-RAY DIFFRACTIONr_chiral_restr0.1210.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212493
X-RAY DIFFRACTIONr_mcbond_it0.9441.52168
X-RAY DIFFRACTIONr_mcangle_it1.74623518
X-RAY DIFFRACTIONr_scbond_it3.0331219
X-RAY DIFFRACTIONr_scangle_it4.8964.51096
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 129 -
Rwork0.33 2505 -
all-2634 -
obs--74.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.076-0.9006-0.53821.42820.7210.68870.0432-0.16150.1630.09340.0726-0.08370.0740.0216-0.11570.0631-0.0322-0.01580.0475-0.02530.0765-1.56920.875-1.215
28.30124.40761.5425.88445.132110.99930.4909-0.84050.35470.4824-0.59320.98570.3189-0.91610.10220.2529-0.0124-0.02550.29720.0130.408-2.2973.754-9.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 496
2X-RAY DIFFRACTION2B201 - 207

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