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- PDB-8he3: Crystal structure of importin-alpha1 bound to the HIF-1alpha nucl... -

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Basic information

Entry
Database: PDB / ID: 8he3
TitleCrystal structure of importin-alpha1 bound to the HIF-1alpha nuclear localization signal (delta 724-751)
Components
  • Hypoxia-inducible factor 1-alpha
  • Importin subunit alpha-1
KeywordsTRANSPORT PROTEIN / NLS
Function / homology
Function and homology information


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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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 ...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 / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,8328
Polymers48,2552
Non-polymers5766
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-62 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.820, 89.650, 100.170
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


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


Mass: 1881.276 Da / Num. of mol.: 1 / Mutation: deletion mutation 724-751
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1A / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: ammonium sulfate, 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: Feb 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→38.24 Å / Num. obs: 56412 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3558 / CC1/2: 0.567 / % possible all: 99.9

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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: 1.9→38.235 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 2863 5.08 %
Rwork0.1887 --
obs0.1897 56323 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 30 326 3631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043356
X-RAY DIFFRACTIONf_angle_d0.764573
X-RAY DIFFRACTIONf_dihedral_angle_d2.6772026
X-RAY DIFFRACTIONf_chiral_restr0.044547
X-RAY DIFFRACTIONf_plane_restr0.005581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93280.3671490.32872602X-RAY DIFFRACTION100
1.9328-1.9680.29931680.28452618X-RAY DIFFRACTION100
1.968-2.00580.271340.26442647X-RAY DIFFRACTION100
2.0058-2.04680.24691170.24322668X-RAY DIFFRACTION100
2.0468-2.09130.24531620.23582619X-RAY DIFFRACTION99
2.0913-2.13990.25491290.22262637X-RAY DIFFRACTION99
2.1399-2.19340.25621380.22292649X-RAY DIFFRACTION100
2.1934-2.25270.24331440.19982659X-RAY DIFFRACTION100
2.2527-2.3190.21761260.19092664X-RAY DIFFRACTION100
2.319-2.39380.24021480.19212670X-RAY DIFFRACTION100
2.3938-2.47940.22311340.18282664X-RAY DIFFRACTION100
2.4794-2.57860.23191430.18662646X-RAY DIFFRACTION100
2.5786-2.6960.21331320.19462689X-RAY DIFFRACTION100
2.696-2.83810.22771490.18222676X-RAY DIFFRACTION100
2.8381-3.01580.20791470.19192659X-RAY DIFFRACTION99
3.0158-3.24850.22141650.1882650X-RAY DIFFRACTION99
3.2485-3.57520.18191390.17722719X-RAY DIFFRACTION100
3.5752-4.09210.14941470.15442736X-RAY DIFFRACTION100
4.0921-5.15360.1891380.15712747X-RAY DIFFRACTION100
5.1536-38.2350.18061540.19092841X-RAY DIFFRACTION98

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