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- PDB-1ee4: CRYSTAL STRUCTURE OF YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMP... -

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Basic information

Entry
Database: PDB / ID: 1ee4
TitleCRYSTAL STRUCTURE OF YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A C-MYC NLS PEPTIDE
Components
  • KARYOPHERIN ALPHA
  • MYC PROTO-ONCOGENE PROTEIN
KeywordsTRANSPORT PROTEIN / ARM repeat
Function / homology
Function and homology information


proteasome localization / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling ...proteasome localization / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / import into nucleus / negative regulation of cell division / negative regulation of monocyte differentiation / DNA methylation-dependent heterochromatin formation / Transcription of E2F targets under negative control by DREAM complex / protein-DNA complex disassembly / transcription regulator activator activity / NLS-dependent protein nuclear import complex / response to growth factor / protein targeting to membrane / negative regulation of stress-activated MAPK cascade / regulation of telomere maintenance / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / chromosome organization / Cyclin E associated events during G1/S transition / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of telomerase activity / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / protein import into nucleus / Transcriptional regulation of granulopoiesis / cellular response to UV / disordered domain specific binding / positive regulation of fibroblast proliferation / MAPK cascade / cellular response to xenobiotic stimulus / nuclear envelope / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / Estrogen-dependent gene expression / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / positive regulation of cell population proliferation / chromatin / protein-containing complex binding / positive regulation of gene expression / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-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 / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Myc proto-oncogene protein / Importin subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsConti, E.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha.
Authors: Conti, E. / Kuriyan, J.
History
DepositionJan 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KARYOPHERIN ALPHA
C: MYC PROTO-ONCOGENE PROTEIN
D: MYC PROTO-ONCOGENE PROTEIN
B: KARYOPHERIN ALPHA
E: MYC PROTO-ONCOGENE PROTEIN
F: MYC PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)97,7426
Polymers97,7426
Non-polymers00
Water5,405300
1
A: KARYOPHERIN ALPHA
C: MYC PROTO-ONCOGENE PROTEIN
D: MYC PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)48,8713
Polymers48,8713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KARYOPHERIN ALPHA
E: MYC PROTO-ONCOGENE PROTEIN
F: MYC PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)48,8713
Polymers48,8713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.680, 85.850, 117.500
Angle α, β, γ (deg.)90.00, 93.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KARYOPHERIN ALPHA / SERINE-RICH RNA POLYMERASE I SUPPRESSOR PROTEIN


Mass: 46870.527 Da / Num. of mol.: 2 / Fragment: ARMADILLO DOMAIN / Mutation: Y397D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q02821
#2: Protein/peptide
MYC PROTO-ONCOGENE PROTEIN


Mass: 1000.215 Da / Num. of mol.: 4
Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) AT THE LARGER (FUNCTIONAL) BINDING SITE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01106
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300
Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) AT THE SMALLER BINDING SITE
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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2100 mMTris-HCl1reservoir
3200 mMsodium acetate1reservoir
430 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 47949 / % possible obs: 96.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→30 Å
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 47949 / Num. measured all: 152954
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 6.6

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber /
RfactorSelection details
Rfree0.277 random 5%
Rwork0.246 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6691 0 0 300 6991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.74
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS

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