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- PDB-1qgk: STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA -

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Basic information

Entry
Database: PDB / ID: 1qgk
TitleSTRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA
Components
  • PROTEIN (IMPORTIN ALPHA-2 SUBUNIT)
  • PROTEIN (IMPORTIN BETA SUBUNIT)
KeywordsTRANSPORT RECEPTOR / NUCLEAR IMPORT / HEAT MOTIF / NLS-BINDING
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / astral microtubule organization / establishment of mitotic spindle localization / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / astral microtubule organization / establishment of mitotic spindle localization / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / DNA metabolic process / nuclear localization sequence binding / CaMK IV-mediated phosphorylation of CREB / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / positive regulation of type I interferon production / mitotic spindle assembly / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / ISG15 antiviral mechanism / histone deacetylase binding / small GTPase binding / specific granule lumen / cytoplasmic stress granule / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / host cell / nuclear envelope / nuclear membrane / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / protein domain specific binding / Golgi membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin-alpha, importin-beta-binding domain / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Importin-alpha, importin-beta-binding domain / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, 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. / HEAT repeat profile. / HEAT, type 2 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsCingolani, G. / Petosa, C. / Weis, K. / Muller, C.W.
CitationJournal: Nature / Year: 1999
Title: Structure of importin-beta bound to the IBB domain of importin-alpha.
Authors: Cingolani, G. / Petosa, C. / Weis, K. / Muller, C.W.
History
DepositionApr 29, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (IMPORTIN BETA SUBUNIT)
B: PROTEIN (IMPORTIN ALPHA-2 SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)102,7072
Polymers102,7072
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-6 kcal/mol
Surface area40880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.584, 97.606, 83.194
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (IMPORTIN BETA SUBUNIT) / KARYOPHERIN BETA-1 / NUCLEAR FACTOR P97 / IMPORTIN B


Mass: 97323.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PEQ60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q14974
#2: Protein/peptide PROTEIN (IMPORTIN ALPHA-2 SUBUNIT) / IMPORTIN ALPHA-2 SUBUNIT / KARYOPHERIN ALPHA-2 SUBUNIT / SRP1-ALPHA


Mass: 5383.339 Da / Num. of mol.: 1 / Fragment: IBB DOMAIN / Source method: obtained synthetically
Details: This protein is chemically synthesized. The sequence of this protein is naturally found in the cytoplasm of homo sapiens (human).
References: UniProt: P52292
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.55 Å3/Da / Density % sol: 51.4 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
218-22 %PEG80001reservoir
350 mMpotassium acetate1reservoir
410 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 34788 / % possible obs: 97.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 15.7
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.302 / % possible all: 97.5
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1759 5 %RANDOM
Rwork0.221 ---
obs-34788 97.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 0 44 7229
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.41.5
X-RAY DIFFRACTIONc_mcangle_it52
X-RAY DIFFRACTIONc_scbond_it5.72
X-RAY DIFFRACTIONc_scangle_it7.92.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PA
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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