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- PDB-3zkv: Importin13 cytosolic state -

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Basic information

Entry
Database: PDB / ID: 3zkv
TitleImportin13 cytosolic state
ComponentsCADMUS
KeywordsTRANSPORT PROTEIN / ACTIVE TRANSPORT / CELL NUCLEUS / KARYOPHERINS NUCLEOCYTOPLASMIC TRANSPORT
Function / homology
Function and homology information


phototaxis / neuron-neuron synaptic transmission / import into nucleus / NLS-dependent protein nuclear import complex / positive regulation of protein-containing complex disassembly / nuclear export / modulation of chemical synaptic transmission / small GTPase binding / protein import into nucleus / synapse ...phototaxis / neuron-neuron synaptic transmission / import into nucleus / NLS-dependent protein nuclear import complex / positive regulation of protein-containing complex disassembly / nuclear export / modulation of chemical synaptic transmission / small GTPase binding / protein import into nucleus / synapse / nucleus / cytoplasm
Similarity search - Function
Importin 13 repeat / Importin 13, repeat 1 / Importin 13 repeat / Importin 13 repeat / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain ...Importin 13 repeat / Importin 13, repeat 1 / Importin 13 repeat / Importin 13 repeat / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGruenwald, M. / Lazzaretti, D. / Bono, F.
CitationJournal: Embo J. / Year: 2013
Title: Structural Basis for the Nuclear Export Activity of Importin13.
Authors: Grunwald, M. / Lazzaretti, D. / Bono, F.
History
DepositionJan 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CADMUS


Theoretical massNumber of molelcules
Total (without water)111,4361
Polymers111,4361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.720, 167.720, 95.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CADMUS / LD35896P / IMPORTIN13


Mass: 111436.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9VEC5

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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: 3.06 Å3/Da / Density % sol: 59.79 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0409
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0409 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 27903 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.9 % / Biso Wilson estimate: 92.72 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 2.28 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X1G

2x1g


Resolution: 3→46.517 Å / SU ML: 0.45 / σ(F): 2.03 / Phase error: 32.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3108 1394 5 %
Rwork0.2718 --
obs0.2738 27853 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.64 Å2
Refinement stepCycle: LAST / Resolution: 3→46.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 0 0 0 6081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046216
X-RAY DIFFRACTIONf_angle_d0.8098528
X-RAY DIFFRACTIONf_dihedral_angle_d13.5372000
X-RAY DIFFRACTIONf_chiral_restr0.0521040
X-RAY DIFFRACTIONf_plane_restr0.0041105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.38481370.35982584X-RAY DIFFRACTION100
3.1072-3.23160.36171360.34732593X-RAY DIFFRACTION100
3.2316-3.37860.34831370.32562603X-RAY DIFFRACTION100
3.3786-3.55670.32251380.30022608X-RAY DIFFRACTION100
3.5567-3.77950.31221380.28072618X-RAY DIFFRACTION100
3.7795-4.07110.34321360.26842611X-RAY DIFFRACTION100
4.0711-4.48050.28651400.25432654X-RAY DIFFRACTION100
4.4805-5.12810.26251400.2442655X-RAY DIFFRACTION100
5.1281-6.45820.30471420.31352703X-RAY DIFFRACTION100
6.4582-46.52270.31171500.24052830X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14350.05280.01710.06450.01710.05380.04760.20140.0285-0.0297-0.0902-0.0574-0.10680.0297-0.01360.58720.31280.19230.32150.43030.85094.4652-19.5392-4.068
20.25720.4243-0.20440.5021-0.0440.3687-0.00650.19680.1025-0.00910.16020.00470.1737-0.2190.06710.1420.10370.01690.278-0.07420.179114.1682-62.9248-21.6967
30.01040.0096-0.0630.0468-0.0130.1158-0.02690.1870.05020.03950.2257-0.3873-0.23130.17730.10740.0932-0.26180.12360.2911-0.33920.856639.67-35.2184-45.4781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 54 THROUGH 167 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 168 THROUGH 725 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 726 THROUGH 967 )

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