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- PDB-7rht: Importin alpha 7 delta IBB (KPNA6) -

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Basic information

Entry
Database: PDB / ID: 7rht
TitleImportin alpha 7 delta IBB (KPNA6)
ComponentsImportin subunit alpha-7
KeywordsPROTEIN TRANSPORT / transportin
Function / homology
Function and homology information


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 / positive regulation of cytokine production involved in inflammatory response / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / maternal process involved in female pregnancy / Assembly of the ORC complex at the origin of replication / viral genome replication ...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 / positive regulation of cytokine production involved in inflammatory response / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / maternal process involved in female pregnancy / Assembly of the ORC complex at the origin of replication / viral genome replication / protein import into nucleus / host cell / transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTsimbalyuk, S. / Forwood, J.K.
CitationJournal: Sci Rep / Year: 2022
Title: Structural characterization of human importin alpha 7 in its cargo-free form at 2.5 angstrom resolution.
Authors: Tsimbalyuk, S. / Donnelly, C.M. / Forwood, J.K.
History
DepositionJul 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: 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_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 1.2Oct 25, 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-7


Theoretical massNumber of molelcules
Total (without water)52,9781
Polymers52,9781
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.850, 75.840, 88.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-7 / Karyopherin subunit alpha-6


Mass: 52978.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA6, IPOA7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60684
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES monohydrate pH 6.5, 12% PEG20000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→24.77 Å / Num. obs: 15096 / % possible obs: 97.2 % / Redundancy: 5.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 2 / Num. unique obs: 1703 / CC1/2: 0.474

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UAD

4uad


Resolution: 2.5→24.77 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 751 4.98 %
Rwork0.2092 14319 -
obs0.2105 15070 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.66 Å2 / Biso mean: 52.5151 Å2 / Biso min: 17.92 Å2
Refinement stepCycle: final / Resolution: 2.5→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 34 3325
Biso mean---44.7 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033347
X-RAY DIFFRACTIONf_angle_d0.4914549
X-RAY DIFFRACTIONf_dihedral_angle_d11.2841243
X-RAY DIFFRACTIONf_chiral_restr0.034539
X-RAY DIFFRACTIONf_plane_restr0.004587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.690.32741380.28652879301798
2.69-2.960.30571620.25112867302998
2.96-3.390.26541620.23352856301898
3.39-4.270.19831520.18682849300195
4.27-24.770.20341370.18012868300591

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