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- PDB-5vqi: Nuclear transport of the Neurospora crassa NIT2 transcription fac... -

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Basic information

Entry
Database: PDB / ID: 5vqi
TitleNuclear transport of the Neurospora crassa NIT2 transcription factor is mediated by Importin-alpha
Components
  • Importin subunit alpha
  • Nuclear localization sequence of NIT2 transcription factor (NIT2-NLS)
KeywordsPROTEIN TRANSPORT / Importin-alpha / nuclear tranport / transcription factor / Neurospora crassa / NIT2
Function / homology
Function and homology information


nuclear import signal receptor activity / nitrate assimilation / protein import into nucleus / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Importin subunit alpha / Atypical Arm repeat ...Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / 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 / Zinc finger, NHR/GATA-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nitrogen catabolic enzyme regulatory protein / Importin subunit alpha
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsBernardes, N.E. / Fontes, M.R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/10289-0 Brazil
CitationJournal: Biochem. J. / Year: 2017
Title: Nuclear transport of the Neurospora crassa NIT-2 transcription factor is mediated by importin-alpha.
Authors: Bernardes, N.E. / Takeda, A.A.S. / Dreyer, T.R. / Cupertino, F.B. / Virgilio, S. / Pante, N. / Bertolini, M.C. / Fontes, M.R.M.
History
DepositionMay 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha
A: Nuclear localization sequence of NIT2 transcription factor (NIT2-NLS)
C: Nuclear localization sequence of NIT2 transcription factor (NIT2-NLS)


Theoretical massNumber of molelcules
Total (without water)56,7563
Polymers56,7563
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint6 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.034, 63.706, 183.635
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 /


Mass: 53602.625 Da / Num. of mol.: 1 / Fragment: unp residues 75-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: 3H10.030, GE21DRAFT_7666 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C2K9
#2: Protein/peptide Nuclear localization sequence of NIT2 transcription factor (NIT2-NLS)


Mass: 1576.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Neurospora crassa (fungus) / References: UniProt: P19212*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 mM Bicine pH 8.5 and 20% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1,45
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
2451
ReflectionResolution: 2.5→45.91 Å / Num. obs: 18973 / % possible obs: 99.71 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.263 / Net I/σ(I): 5.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MxCuBEdata collection
HKL-2000data processing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RXH

4rxh


Resolution: 2.501→45.909 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.85
RfactorNum. reflection% reflection
Rfree0.2461 948 5 %
Rwork0.1795 --
obs0.1828 18962 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→45.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 175 3440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083316
X-RAY DIFFRACTIONf_angle_d1.1964507
X-RAY DIFFRACTIONf_dihedral_angle_d13.8041215
X-RAY DIFFRACTIONf_chiral_restr0.042541
X-RAY DIFFRACTIONf_plane_restr0.006577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.63280.31231290.22692473X-RAY DIFFRACTION98
2.6328-2.79770.30091330.22852527X-RAY DIFFRACTION100
2.7977-3.01370.28921340.22082555X-RAY DIFFRACTION100
3.0137-3.31690.28421340.2082539X-RAY DIFFRACTION100
3.3169-3.79670.2781360.18712575X-RAY DIFFRACTION100
3.7967-4.78260.21431370.14962589X-RAY DIFFRACTION100
4.7826-45.91650.19711450.15032756X-RAY DIFFRACTION100

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