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- PDB-7vpu: Crystal structure of the ligand-binding domain of L. thermotolera... -

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Basic information

Entry
Database: PDB / ID: 7vpu
TitleCrystal structure of the ligand-binding domain of L. thermotolerans Upc2 in complex with ergosterol
ComponentsSterol uptake control protein 2 (Upc2)
KeywordsTRANSCRIPTION / ergosterol / transcription factor / ligand-binding / zinc finger
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / zinc ion binding / nucleus
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
Similarity search - Domain/homology
ERGOSTEROL / KLTH0F07854p
Similarity search - Component
Biological speciesLachancea thermotolerans CBS 6340 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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 1.0Aug 24, 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

Downloads & links

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Assembly

Deposited unit
A: Sterol uptake control protein 2 (Upc2)
B: Sterol uptake control protein 2 (Upc2)
C: Sterol uptake control protein 2 (Upc2)
D: Sterol uptake control protein 2 (Upc2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0568
Polymers148,4694
Non-polymers1,5874
Water0
1
A: Sterol uptake control protein 2 (Upc2)
B: Sterol uptake control protein 2 (Upc2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0284
Polymers74,2352
Non-polymers7932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-15 kcal/mol
Surface area26410 Å2
MethodPISA
2
C: Sterol uptake control protein 2 (Upc2)
D: Sterol uptake control protein 2 (Upc2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0284
Polymers74,2352
Non-polymers7932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.379, 147.127, 90.948
Angle α, β, γ (deg.)90.000, 108.325, 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
Sterol uptake control protein 2 (Upc2)


Mass: 37117.344 Da / Num. of mol.: 4 / Mutation: 587-600 deletion, S599V, M600D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans CBS 6340 (fungus)
Strain: CBS 6340 / Gene: KLTH0F07854g / 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: C5DKV6
#2: Chemical
ChemComp-ERG / ERGOSTEROL / Ergosterol


Mass: 396.648 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H44O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M Na-Acetate pH 4.0, 15% PEG 20000, 0.2 M NaNO3

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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: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 49148 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 58.87 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 33
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2446 / % possible all: 100

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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: 4N9N

4n9n


Resolution: 2.59→24.31 Å / SU ML: 0.366 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 2485 5.06 %
Rwork0.2289 46617 -
obs0.2314 49102 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.82 Å2
Refinement stepCycle: LAST / Resolution: 2.59→24.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8512 0 116 0 8628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01228834
X-RAY DIFFRACTIONf_angle_d2.139412019
X-RAY DIFFRACTIONf_chiral_restr0.16141404
X-RAY DIFFRACTIONf_plane_restr0.0151483
X-RAY DIFFRACTIONf_dihedral_angle_d9.99445232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.640.35931070.30952321X-RAY DIFFRACTION88.61
2.64-2.690.35781410.29652617X-RAY DIFFRACTION99.86
2.69-2.750.3411260.29462628X-RAY DIFFRACTION99.96
2.75-2.820.40891370.30942623X-RAY DIFFRACTION99.93
2.82-2.890.35031400.30042597X-RAY DIFFRACTION99.89
2.89-2.960.35441440.29392611X-RAY DIFFRACTION99.93
2.96-3.050.33911470.2952640X-RAY DIFFRACTION100
3.05-3.150.35391330.28632606X-RAY DIFFRACTION99.96
3.15-3.260.3551330.28282643X-RAY DIFFRACTION100
3.26-3.390.31641500.26912622X-RAY DIFFRACTION100
3.39-3.550.31041580.25522598X-RAY DIFFRACTION99.86
3.55-3.730.29661490.22362617X-RAY DIFFRACTION99.96
3.73-3.970.23061340.21712636X-RAY DIFFRACTION99.82
3.97-4.270.22961300.19392635X-RAY DIFFRACTION99.96
4.27-4.70.21711490.18142625X-RAY DIFFRACTION99.96
4.7-5.370.24611660.18782624X-RAY DIFFRACTION99.82
5.37-6.740.25361300.22792634X-RAY DIFFRACTION99.96
6.74-24.310.25051110.19282340X-RAY DIFFRACTION86.49

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