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- PDB-1f59: IMPORTIN-BETA-FXFG NUCLEOPORIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1f59
TitleIMPORTIN-BETA-FXFG NUCLEOPORIN COMPLEX
Components
  • FXFG NUCLEOPORIN REPEATS
  • IMPORTIN BETA-1
KeywordsTRANSPORT PROTEIN RECEPTOR / Protein-protein complex
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 / importin-alpha family protein binding / astral microtubule organization / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / NS1 Mediated Effects on Host Pathways ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / importin-alpha family protein binding / astral microtubule organization / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / Apoptosis induced DNA fragmentation / Initiation of Nuclear Envelope (NE) Reformation / nuclear localization sequence binding / ribosomal protein import into nucleus / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / mitotic metaphase chromosome alignment / mitotic spindle assembly / 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 / protein import into nucleus / cytoplasmic stress granule / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / Neutrophil degranulation / enzyme binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
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 / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats ...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 / HEAT repeat profile. / HEAT, type 2 / 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 beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsBayliss, R. / Littlewood, T. / Stewart, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural basis for the interaction between FxFG nucleoporin repeats and importin-beta in nuclear trafficking.
Authors: Bayliss, R. / Littlewood, T. / Stewart, M.
History
DepositionJun 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: 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: IMPORTIN BETA-1
B: IMPORTIN BETA-1
C: FXFG NUCLEOPORIN REPEATS
D: FXFG NUCLEOPORIN REPEATS


Theoretical massNumber of molelcules
Total (without water)104,1444
Polymers104,1444
Non-polymers00
Water00
1
A: IMPORTIN BETA-1
C: FXFG NUCLEOPORIN REPEATS


Theoretical massNumber of molelcules
Total (without water)52,0722
Polymers52,0722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-11 kcal/mol
Surface area21940 Å2
MethodPISA
2
B: IMPORTIN BETA-1
D: FXFG NUCLEOPORIN REPEATS


Theoretical massNumber of molelcules
Total (without water)52,0722
Polymers52,0722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.246, 211.790, 125.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein IMPORTIN BETA-1


Mass: 49385.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q14974
#2: Protein/peptide FXFG NUCLEOPORIN REPEATS / NSP1P


Mass: 2687.036 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET / Production host: Escherichia coli (E. coli)

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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: 4.3 Å3/Da / Density % sol: 71.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulphate, ammonium acetate, dtt, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.1 mg/ml1-4421drop0.003ml
211 mg/mlFF51drop0.001ml
31.28-1.33 Mammonium sulfate1drop
4200 mMammonium acetate1drop
51.24 Mammonium sulfate1reservoir
6100 mMammonium acetate1reservoir
750 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 45165 / Num. obs: 31295 / % possible obs: 69.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.176 / Num. unique all: 699 / % possible all: 10.8
Reflection
*PLUS
Num. measured all: 144382
Reflection shell
*PLUS
% possible obs: 10.8 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.8→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: mlf target
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3130 -random
Rwork0.225 ---
all-45165 --
obs-31295 69.1 %-
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7159 0 0 0 7159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.009

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