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- PDB-6mjl: Crystal structure of ChREBP NLS peptide bound to importin alpha. -

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Basic information

Entry
Database: PDB / ID: 6mjl
TitleCrystal structure of ChREBP NLS peptide bound to importin alpha.
Components
  • ChREBP Peptide ASN-TYR-TRP-LYS-ARG-ARG-ILE-GLU-VAL
  • Importin subunit alpha-1
KeywordsTRANSCRIPTION/PEPTIDE / ChREBP / Importin alpha / TRANSCRIPTION / TRANSCRIPTION-PEPTIDE complex
Function / homology
Function and homology information


carbohydrate response element binding / glucose mediated signaling pathway / PKA-mediated phosphorylation of key metabolic factors / AMPK inhibits chREBP transcriptional activation activity / PP2A-mediated dephosphorylation of key metabolic factors / positive regulation of transcription from RNA polymerase II promoter by glucose / ChREBP activates metabolic gene expression / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle ...carbohydrate response element binding / glucose mediated signaling pathway / PKA-mediated phosphorylation of key metabolic factors / AMPK inhibits chREBP transcriptional activation activity / PP2A-mediated dephosphorylation of key metabolic factors / positive regulation of transcription from RNA polymerase II promoter by glucose / ChREBP activates metabolic gene expression / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / positive regulation of fatty acid biosynthetic process / NLS-dependent protein nuclear import complex / negative regulation of oxidative phosphorylation / postsynapse to nucleus signaling pathway / triglyceride homeostasis / lipid biosynthetic process / nuclear import signal receptor activity / nuclear localization sequence binding / DNA-binding transcription activator activity / NLS-bearing protein import into nucleus / negative regulation of peptidyl-serine phosphorylation / anatomical structure morphogenesis / fatty acid homeostasis / energy homeostasis / positive regulation of lipid biosynthetic process / positive regulation of glycolytic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / cytoplasmic stress granule / RNA polymerase II transcription regulator complex / protein import into nucleus / host cell / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / glutamatergic synapse / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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
Importin subunit alpha-1 / Carbohydrate-responsive element-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsJung, H. / Uyeda, K.
CitationJournal: Biochem.J. / Year: 2020
Title: The structure of importin alpha and the nuclear localization peptide of ChREBP, and small compound inhibitors of ChREBP-importin alpha interactions.
Authors: Jung, H. / Takeshima, T. / Nakagawa, T. / MacMillan, K.S. / Wynn, R.M. / Wang, H. / Sakiyama, H. / Wei, S. / Li, Y. / Bruick, R.K. / Posner, B.A. / De Brabander, J.K. / Uyeda, K.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 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

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Assembly

Deposited unit
B: Importin subunit alpha-1
A: ChREBP Peptide ASN-TYR-TRP-LYS-ARG-ARG-ILE-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)47,4102
Polymers47,4102
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint1 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.434, 89.691, 96.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 46143.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Importin alpha delta IBB / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide ChREBP Peptide ASN-TYR-TRP-LYS-ARG-ARG-ILE-GLU-VAL


Mass: 1266.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NP71*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 500 mM Na Citrate 10 mM DTT 20 mM HEPES pH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23621 / % possible obs: 97.6 % / Redundancy: 3.9 % / Rsym value: 0.08 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.54 Å / Rsym value: 0.542

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.5→42.434 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.2444 981 4.89 %
Rwork0.1977 --
obs0.1999 20071 84.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 71 3401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083389
X-RAY DIFFRACTIONf_angle_d0.9624614
X-RAY DIFFRACTIONf_dihedral_angle_d2.8782052
X-RAY DIFFRACTIONf_chiral_restr0.05554
X-RAY DIFFRACTIONf_plane_restr0.006589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.63190.3024840.21981469X-RAY DIFFRACTION46
2.6319-2.79680.2256960.22162178X-RAY DIFFRACTION68
2.7968-3.01270.27831250.22812695X-RAY DIFFRACTION84
3.0127-3.31580.28511560.22243022X-RAY DIFFRACTION94
3.3158-3.79530.24541750.19563175X-RAY DIFFRACTION99
3.7953-4.78070.2361750.17093205X-RAY DIFFRACTION98
4.7807-42.44030.21711700.19253346X-RAY DIFFRACTION98

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