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- PDB-1qgr: STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN AL... -

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Basic information

Entry
Database: PDB / ID: 1qgr
TitleSTRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA (II CRYSTAL FORM, GROWN AT LOW PH)
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 / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / Apoptosis induced DNA fragmentation / nuclear localization sequence binding / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / 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 / CaMK IV-mediated phosphorylation of CREB / DNA metabolic process / mitotic metaphase chromosome alignment / mitotic spindle assembly / positive regulation of type I interferon production / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / small GTPase binding / ISG15 antiviral mechanism / specific granule lumen / histone deacetylase binding / cytoplasmic stress granule / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / host cell / nuclear membrane / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Golgi membrane / protein domain specific binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / 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 / 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 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMay 4, 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 1.3Aug 16, 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: PROTEIN (IMPORTIN BETA SUBUNIT)
B: PROTEIN (IMPORTIN ALPHA-2 SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)100,7302
Polymers100,7302
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.896, 101.167, 83.831
Angle α, β, γ (deg.)90.00, 87.86, 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: 3406.046 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.: 186 / 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: 2.43 Å3/Da / Density % sol: 48.1 %
Crystal growpH: 3.9 / Details: pH 3.9
Crystal
*PLUS
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116-20 %PEG800011
250 mMpotassium phosphate11
310 mMbeta-mercaptoethanol11
45 mMsodium iodide11
550 mg/mlprotain11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.997
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 46295 / % possible obs: 98.5 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.37 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / Rsym value: 0.38 / % possible all: 98.5
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB IDCODE 1QGK

1qgk


Resolution: 2.3→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2535 5 %RANDOM
Rwork0.235 ---
obs-46295 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6995 0 0 186 7181
Refine LS restraints
Refine-IDTypeDev ideal
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor obs: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS

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