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- PDB-7vpt: Structure of the C. glabrata importin alpha ARM domain - Upc2 NLS... -

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Basic information

Entry
Database: PDB / ID: 7vpt
TitleStructure of the C. glabrata importin alpha ARM domain - Upc2 NLS fusion
ComponentsC. glabrata importin alpha ARM domain - Upc2 NLS fusion
KeywordsPROTEIN TRANSPORT / importin / nuclear transport / protein sorting
Function / homology
Function and homology information


proteasome localization / NLS-dependent protein nuclear import complex / ergosterol biosynthetic process / protein targeting to membrane / nuclear import signal receptor activity / NLS-bearing protein import into nucleus / disordered domain specific binding / nuclear envelope / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...proteasome localization / NLS-dependent protein nuclear import complex / ergosterol biosynthetic process / protein targeting to membrane / nuclear import signal receptor activity / NLS-bearing protein import into nucleus / disordered domain specific binding / nuclear envelope / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein-containing complex binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / membrane / nucleus / cytosol
Similarity search - Function
Fungal transcription factor / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Importin subunit alpha / Atypical Arm repeat ...Fungal transcription factor / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha / Zn(2)-C6 fungal-type domain-containing protein
Similarity search - Component
Biological species[Candida] glabrata CBS 138 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTan, L. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1085530 Korea, Republic Of
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Structural basis for activation of fungal sterol receptor Upc2 and azole resistance.
Authors: Tan, L. / Chen, L. / Yang, H. / Jin, B. / Kim, G. / Im, Y.J.
History
DepositionOct 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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: C. glabrata importin alpha ARM domain - Upc2 NLS fusion


Theoretical massNumber of molelcules
Total (without water)52,1731
Polymers52,1731
Non-polymers00
Water99155
1
A: C. glabrata importin alpha ARM domain - Upc2 NLS fusion

A: C. glabrata importin alpha ARM domain - Upc2 NLS fusion

A: C. glabrata importin alpha ARM domain - Upc2 NLS fusion


Theoretical massNumber of molelcules
Total (without water)156,5203
Polymers156,5203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area11490 Å2
ΔGint-5 kcal/mol
Surface area57090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.025, 119.025, 74.511
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein C. glabrata importin alpha ARM domain - Upc2 NLS fusion


Mass: 52173.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] glabrata CBS 138 (fungus) / Strain: CBS 138 / Gene: CAGL0J11440g, UPC2A / Plasmid: pHIS2-Thr
Details (production host): N-terminal cleavable hexa-histidine
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6FNI4, UniProt: Q6FX18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl pH 8.0, 30% PEG 400

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20974 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 36.57 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 46.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 12 / Num. unique obs: 1048

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XGR

4xgr


Resolution: 2.5→34.53 Å / SU ML: 0.2696 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2661 1979 9.45 %
Rwork0.1999 18955 -
obs0.2061 20934 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 0 55 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923685
X-RAY DIFFRACTIONf_angle_d1.12325001
X-RAY DIFFRACTIONf_chiral_restr0.0635589
X-RAY DIFFRACTIONf_plane_restr0.0083646
X-RAY DIFFRACTIONf_dihedral_angle_d21.92221382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.29491390.20781345X-RAY DIFFRACTION99.73
2.56-2.630.28851450.21311345X-RAY DIFFRACTION99.93
2.63-2.710.29621420.20871350X-RAY DIFFRACTION99.87
2.71-2.80.34281410.20741327X-RAY DIFFRACTION99.8
2.8-2.90.25521400.22141359X-RAY DIFFRACTION99.8
2.9-3.010.32741400.22811324X-RAY DIFFRACTION99.86
3.01-3.150.26991410.221360X-RAY DIFFRACTION99.93
3.15-3.310.32151390.22711356X-RAY DIFFRACTION100
3.31-3.520.27521410.21361361X-RAY DIFFRACTION99.93
3.52-3.790.25421360.20951364X-RAY DIFFRACTION99.87
3.79-4.170.25711400.17181342X-RAY DIFFRACTION99.87
4.17-4.780.26261460.16961368X-RAY DIFFRACTION99.87
4.78-6.010.25181470.20361359X-RAY DIFFRACTION99.87
6.01-34.530.21241420.18911395X-RAY DIFFRACTION99.29

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