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- PDB-8he0: Crystal structure of importin-alpha1 bound to the HIF-1alpha nucl... -

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Basic information

Entry
Database: PDB / ID: 8he0
TitleCrystal structure of importin-alpha1 bound to the HIF-1alpha nuclear localization signal (wild-type)
Components
  • Hypoxia-inducible factor 1-alpha
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / NLS
Function / homology
Function and homology information


epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation / : / hemoglobin biosynthetic process ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation / : / hemoglobin biosynthetic process / cardiac ventricle morphogenesis / connective tissue replacement involved in inflammatory response wound healing / negative regulation of mesenchymal cell apoptotic process / negative regulation of growth / positive regulation of hormone biosynthetic process / intestinal epithelial cell maturation / retina vasculature development in camera-type eye / Cellular response to hypoxia / mesenchymal cell apoptotic process / Sensing of DNA Double Strand Breaks / regulation of protein neddylation / negative regulation of bone mineralization / PTK6 Expression / intracellular oxygen homeostasis / collagen metabolic process / entry of viral genome into host nucleus through nuclear pore complex via importin / B-1 B cell homeostasis / vascular endothelial growth factor production / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / dopaminergic neuron differentiation / postsynapse to nucleus signaling pathway / transcription regulator activator activity / STAT3 nuclear events downstream of ALK signaling / negative regulation of thymocyte apoptotic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / lactate metabolic process / positive regulation of cytokine production involved in inflammatory response / negative regulation of TOR signaling / insulin secretion involved in cellular response to glucose stimulus / positive regulation of vascular endothelial growth factor receptor signaling pathway / response to iron ion / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / nuclear import signal receptor activity / embryonic hemopoiesis / regulation of glycolytic process / motile cilium / DNA-binding transcription repressor activity / muscle cell cellular homeostasis / digestive tract morphogenesis / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / response to muscle activity / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / bone mineralization / E-box binding / intracellular glucose homeostasis / heart looping / outflow tract morphogenesis / TOR signaling / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of macroautophagy / cellular response to interleukin-1 / positive regulation of epithelial cell migration / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / chondrocyte differentiation / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / positive regulation of chemokine production / positive regulation of endothelial cell proliferation / lactation / axon cytoplasm / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / response to reactive oxygen species / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / transcription coactivator binding / euchromatin / visual learning / cerebral cortex development / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to virus / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / RNA polymerase II transcription regulator complex / protein import into nucleus / cytoplasmic stress granule / positive regulation of angiogenesis / p53 binding / :
Similarity search - Function
Hypoxia-inducible factor-1 alpha / Hypoxia-inducible factor 1-alpha bHLH domain / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold / Importin subunit alpha / Atypical Arm repeat ...Hypoxia-inducible factor-1 alpha / Hypoxia-inducible factor 1-alpha bHLH domain / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold / 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 / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Hypoxia-inducible factor 1-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatsuura, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K06511 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structures of importin-alpha bound to the wild-type and an internal deletion mutant of the bipartite nuclear localization signal of HIF-1 alpha.
Authors: Matsuura, Y. / Miyawaki, K.
History
DepositionNov 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: 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 / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: Hypoxia-inducible factor 1-alpha


Theoretical massNumber of molelcules
Total (without water)51,1202
Polymers51,1202
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint3 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.750, 90.740, 97.660
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: 46374.152 Da / Num. of mol.: 1 / Fragment: UNP residues 72-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Hypoxia-inducible factor 1-alpha / HIF-1-alpha / HIF1-alpha


Mass: 4745.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q16665
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: tri-sodium citrate, HEPES, DTT

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→25.07 Å / Num. obs: 65167 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3807 / CC1/2: 0.705 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
MOSFLMdata reduction
SCALEITdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IU7

6iu7


Resolution: 1.8→25.07 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 3440 5.29 %
Rwork0.1828 --
obs0.1836 65075 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→25.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 0 355 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.6774651
X-RAY DIFFRACTIONf_dihedral_angle_d13.3552092
X-RAY DIFFRACTIONf_chiral_restr0.043556
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shellResolution: 1.8→1.8247 Å
RfactorNum. reflection% reflection
Rfree0.3246 121 -
Rwork0.3334 2454 -
obs--100 %

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