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- PDB-1un0: Crystal Structure of Yeast Karyopherin (Importin) alpha in comple... -

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Basic information

Entry
Database: PDB / ID: 1un0
TitleCrystal Structure of Yeast Karyopherin (Importin) alpha in complex with a Nup2p N-terminal fragment
Components
  • IMPORTIN ALPHA SUBUNIT
  • NUCLEOPORIN NUP2
KeywordsNUCLEAR IMPORT / ARMADILLO REPEAT / NUCLEOPORIN / NLS RELEASE / KARYOPHERIN RECYCLING
Function / homology
Function and homology information


proteasome localization / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket ...proteasome localization / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / protein targeting to membrane / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / subtelomeric heterochromatin formation / nuclear pore / protein export from nucleus / GTPase activator activity / small GTPase binding / protein import into nucleus / disordered domain specific binding / nuclear envelope / nuclear membrane / chromosome, telomeric region / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding 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 / Armadillo-like helical / Alpha Horseshoe / PH-like domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP2 / Importin subunit alpha
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMatsuura, Y. / Lange, A. / Harreman, M.T. / Corbett, A.H. / Stewart, M.
CitationJournal: Embo J. / Year: 2003
Title: Structural Basis for Nup2P Function in Cargo Release and Karyopherin Recycling in Nuclear Import
Authors: Matsuura, Y. / Lange, A. / Harreman, M.T. / Corbett, A.H. / Stewart, M.
History
DepositionSep 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

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Assembly

Deposited unit
A: IMPORTIN ALPHA SUBUNIT
B: IMPORTIN ALPHA SUBUNIT
C: NUCLEOPORIN NUP2
D: NUCLEOPORIN NUP2


Theoretical massNumber of molelcules
Total (without water)109,4404
Polymers109,4404
Non-polymers00
Water2,846158
1
A: IMPORTIN ALPHA SUBUNIT
C: NUCLEOPORIN NUP2


Theoretical massNumber of molelcules
Total (without water)54,7202
Polymers54,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IMPORTIN ALPHA SUBUNIT
D: NUCLEOPORIN NUP2


Theoretical massNumber of molelcules
Total (without water)54,7202
Polymers54,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.813, 140.076, 63.990
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 ALPHA SUBUNIT / KAP60P / KARYOPHERIN ALPHA SUBUNIT / SERINE-RICH RNA POLYMERASE I SUPPRESSOR PROTEIN


Mass: 48906.562 Da / Num. of mol.: 2 / Fragment: ARMADILLO REPEAT DOMAIN, RESIDUES 88-530 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02821
#2: Protein NUCLEOPORIN NUP2 / NUP2P / NUCLEAR PORE PROTEIN NUP2 / P95


Mass: 5813.649 Da / Num. of mol.: 2 / Fragment: N-TERMINAL FRAGMENT, RESIDUES 1-51
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32499
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION TYR 397 ASP

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.8
Details: 50 MM HEPES PH 6.8, 0.15 M NACL, 24 % PEG3350, 2 % PEG400
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mg/mlprotein1drop
250 mMHEPES1droppH6.8
30.15 M1dropNaCl
424 %PEG33501drop
52 %PEG4001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 29670 / % possible obs: 97.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. measured all: 76810 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 98.3 % / Num. unique obs: 4308 / Num. measured obs: 10875 / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EE4

1ee4


Resolution: 2.6→20 Å / SU B: 11.435 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.686 / ESU R Free: 0.316
RfactorNum. reflection% reflectionSelection details
Rfree0.25735 1806 5.1 %RANDOM
Rwork0.21566 ---
obs0.21781 33802 97.81 %-
Displacement parametersBiso mean: 49.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---1.57 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7073 0 0 158 7231
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.831

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