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- PDB-4n9n: Crystal Structure of Saccharomyces cerevisiae Upc2 Transcription ... -

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Basic information

Entry
Database: PDB / ID: 4n9n
TitleCrystal Structure of Saccharomyces cerevisiae Upc2 Transcription Factor fused with T4 Lysozyme
ComponentsSterol uptake control protein 2, Lysozyme
KeywordsTRANSCRIPTION / fungal nuclear receptor-like transcription factor / ergosterol binding / nucleus
Function / homology
Function and homology information


positive regulation of sterol import / positive regulation of ergosterol biosynthetic process / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / 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 ...positive regulation of sterol import / positive regulation of ergosterol biosynthetic process / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / 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 / Lysozyme - #40 ...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 / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Endolysin / Sterol uptake control protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsYang, H. / Im, Y.J.
CitationJournal: To be Published
Title: Structural mechanism of ergosterol regulation by fungal sterol nuclear receptor Upc2
Authors: Yang, H. / Tong, J. / Ha, S. / Eom, S.H. / Im, Y.J.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterol uptake control protein 2, Lysozyme
B: Sterol uptake control protein 2, Lysozyme


Theoretical massNumber of molelcules
Total (without water)99,7102
Polymers99,7102
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-16 kcal/mol
Surface area39800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.170, 67.170, 257.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Sterol uptake control protein 2, Lysozyme / Upc2 zinc cluster transcription factor


Mass: 49855.242 Da / Num. of mol.: 2
Fragment: residues 598-714 and 726-878 of Q12151, residues 2-161 of P00720
Mutation: C1054T, C1097A
Source method: isolated from a genetically manipulated source
Details: chimera of Sterol uptake control protein 2 and Lysozyme
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: S288c / Gene: UPC2, E / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12151, UniProt: P00720
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 12.5% PEG 8000, 0.2M sodium citrate, 7.5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 2, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.9→58.17 Å / Num. all: 28846 / Num. obs: 28788 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4194 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→58.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1457995.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1442 5 %RANDOM
Rwork0.251 ---
all0.255 28846 --
obs0.251 28729 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1384 Å2 / ksol: 0.356167 e/Å3
Displacement parametersBiso mean: 66 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å29.82 Å20 Å2
2--1.58 Å20 Å2
3----3.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.9→58.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6800 0 0 29 6829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 217 4.6 %
Rwork0.388 4495 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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