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- PDB-7vps: Crystal structure of the ARM domain of C. glabrata importin alpha -

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Basic information

Entry
Database: PDB / ID: 7vps
TitleCrystal structure of the ARM domain of C. glabrata importin alpha
ComponentsImportin subunit alpha
KeywordsPROTEIN TRANSPORT / importin / nuclear transport / protein sorting
Function / homology
Function and homology information


proteasome localization / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / protein targeting to membrane / disordered domain specific binding / nuclear envelope / protein-containing complex binding / 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
Similarity search - Component
Biological species[Candida] glabrata CBS 138 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 17, 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: Importin subunit alpha
B: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)98,4262
Polymers98,4262
Non-polymers00
Water5,675315
1
A: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)49,2131
Polymers49,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Importin subunit alpha


Theoretical massNumber of molelcules
Total (without water)49,2131
Polymers49,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.650, 62.628, 154.646
Angle α, β, γ (deg.)90.000, 90.023, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Importin subunit alpha


Mass: 49212.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] glabrata CBS 138 (fungus) / Strain: CBS 138 / Plasmid: pHIS2-Thr
Details (production host): N-terminal cleavable hexa-histidine tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6FNI4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris-HCl pH 7.0, 30% PEG 8000, 0.4 M NaCl

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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: 0.97949 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: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 39813 / % possible obs: 97 % / Redundancy: 2.8 % / Biso Wilson estimate: 24.79 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1934 / % possible all: 95.9

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Processing

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

4xgr


Resolution: 2.29→31.31 Å / SU ML: 0.2848 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2705
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2665 2008 5.05 %
Rwork0.2177 37775 -
obs0.2201 39783 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.49 Å2
Refinement stepCycle: LAST / Resolution: 2.29→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6790 0 0 315 7105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01196896
X-RAY DIFFRACTIONf_angle_d1.59399378
X-RAY DIFFRACTIONf_chiral_restr0.07591111
X-RAY DIFFRACTIONf_plane_restr0.01231215
X-RAY DIFFRACTIONf_dihedral_angle_d7.0794238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.31261350.25682523X-RAY DIFFRACTION91.53
2.35-2.410.33241450.2612661X-RAY DIFFRACTION96.23
2.41-2.480.31951480.25792714X-RAY DIFFRACTION97.31
2.48-2.570.33851400.24342679X-RAY DIFFRACTION97.75
2.57-2.660.31221460.2432724X-RAY DIFFRACTION97.19
2.66-2.760.29771360.23282704X-RAY DIFFRACTION97.96
2.76-2.890.34061440.24812733X-RAY DIFFRACTION98.09
2.89-3.040.27661430.24652740X-RAY DIFFRACTION98.06
3.04-3.230.29531430.23992717X-RAY DIFFRACTION97.98
3.23-3.480.29611470.22842734X-RAY DIFFRACTION97.83
3.48-3.830.24911460.20572714X-RAY DIFFRACTION97.38
3.83-4.380.23331440.18072738X-RAY DIFFRACTION96.78
4.38-5.520.19891420.192695X-RAY DIFFRACTION96.14
5.52-31.310.19841490.17762699X-RAY DIFFRACTION93.13

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