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- PDB-7xb5: Structure of the ligand-binding domain of S. cerevisiae Upc2 in f... -

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Basic information

Entry
Database: PDB / ID: 7xb5
TitleStructure of the ligand-binding domain of S. cerevisiae Upc2 in fusion with T4 lysozyme
Componentsfusion protein of Sterol uptake control protein 2 and Endolysin
KeywordsTRANSCRIPTION / ergosterol / transcription factor / ligand-binding / zinc finger
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / host cell cytoplasm / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / host cell cytoplasm / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / membrane / nucleus / cytoplasm
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 / Endolysin T4 type / T4-type lysozyme ...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 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Sterol uptake control protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Escherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 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
DepositionMar 20, 2022Deposition 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: fusion protein of Sterol uptake control protein 2 and Endolysin


Theoretical massNumber of molelcules
Total (without water)52,2541
Polymers52,2541
Non-polymers00
Water0
1
A: fusion protein of Sterol uptake control protein 2 and Endolysin

A: fusion protein of Sterol uptake control protein 2 and Endolysin


Theoretical massNumber of molelcules
Total (without water)104,5082
Polymers104,5082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2200 Å2
ΔGint-26 kcal/mol
Surface area36240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.744, 125.085, 155.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein fusion protein of Sterol uptake control protein 2 and Endolysin / / Mannoprotein regulation by oxygen protein 4 / Lysis protein / Lysozyme / Muramidase


Mass: 52253.812 Da / Num. of mol.: 1 / Mutation: R727G,C769T,C812A,I852R,I925G
Source method: isolated from a genetically manipulated source
Details: The loop residues 715-725 of Upc2 were replaced by bacteriophage T4 Lysozyme (residues 2 - 161) using Val-Asp dipeptide as linkers.
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Escherichia virus T4
Strain: S288c / Gene: UPC2, MOX4, YDR213W, YD8142.14, YD8142B.05, UPC2 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12151, UniProt: P00720, lysozyme

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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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 12.5% PEG 8000, 0.2 M sodium citrate

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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, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.44→50 Å / Num. obs: 8514 / % possible obs: 97.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 105.93 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 32.8
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 418 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N9N

4n9n


Resolution: 3.44→32.98 Å / SU ML: 0.5063 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3008 398 4.69 %
Rwork0.258 8095 -
obs0.2601 8493 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.53 Å2
Refinement stepCycle: LAST / Resolution: 3.44→32.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 0 0 2859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01192921
X-RAY DIFFRACTIONf_angle_d1.72353965
X-RAY DIFFRACTIONf_chiral_restr0.1338456
X-RAY DIFFRACTIONf_plane_restr0.0084498
X-RAY DIFFRACTIONf_dihedral_angle_d18.82331056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.44-3.930.35711380.26832483X-RAY DIFFRACTION90.82
3.93-4.950.29091120.26512750X-RAY DIFFRACTION98.22
4.95-32.980.28671480.25062862X-RAY DIFFRACTION98.92
Refinement TLS params.Method: refined / Origin x: -4.47222941247 Å / Origin y: -20.5726666228 Å / Origin z: 20.2193100025 Å
111213212223313233
T0.762236375491 Å20.0396939967372 Å20.0224941415443 Å2-0.830268101998 Å2-0.0982651128303 Å2--0.560399916866 Å2
L1.76886306476 °22.60534387813 °20.407733967081 °2-6.10636810026 °2-1.15573388805 °2--2.79190122718 °2
S-0.260902217537 Å °0.203373288764 Å °-0.301400618528 Å °-1.13613922857 Å °0.0771192110371 Å °-0.25487972147 Å °0.216416645816 Å °-0.366102757701 Å °0.199005938237 Å °
Refinement TLS groupSelection details: all

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