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- PDB-9jua: The complex of Eny2B and Sgf11 of Drosophila melanogaster -

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Basic information

Entry
Database: PDB / ID: 9jua
TitleThe complex of Eny2B and Sgf11 of Drosophila melanogaster
Components
  • Enhancer of yellow 2b transcription factor
  • SAGA-associated factor 11 homolog
KeywordsTRANSCRIPTION / transcription regulation
Function / homology
Function and homology information


DUBm complex / chromatin insulator sequence binding / transcription export complex 2 / SAGA complex / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / transcription elongation by RNA polymerase II / protein transport / chromatin organization ...DUBm complex / chromatin insulator sequence binding / transcription export complex 2 / SAGA complex / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / transcription elongation by RNA polymerase II / protein transport / chromatin organization / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / SAGA complex, Sgf11 subunit / Sgf11 (transcriptional regulation protein) / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2
Similarity search - Domain/homology
Enhancer of yellow 2b transcription factor / SAGA-associated factor 11 homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBoyko, K.M. / Bonchuk, A.N. / Nikolaeva, A.Y. / Arkova, O.V. / Belova, E.V. / Georgiev, P.G. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-30026 Russian Federation
CitationJournal: To Be Published
Title: The complex of Eny2B and Sgf11 of Drosophila melanogaster
Authors: Boyko, K.M. / Nikolaeva, A.Y. / Bonchuk, A.N. / Arkova, O.V. / Belova, E.V. / Georgiev, P.G. / Popov, V.O.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enhancer of yellow 2b transcription factor
C: Enhancer of yellow 2b transcription factor
B: SAGA-associated factor 11 homolog
D: SAGA-associated factor 11 homolog


Theoretical massNumber of molelcules
Total (without water)30,6514
Polymers30,6514
Non-polymers00
Water00
1
A: Enhancer of yellow 2b transcription factor
B: SAGA-associated factor 11 homolog


Theoretical massNumber of molelcules
Total (without water)15,3262
Polymers15,3262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-22 kcal/mol
Surface area6490 Å2
MethodPISA
2
C: Enhancer of yellow 2b transcription factor
D: SAGA-associated factor 11 homolog


Theoretical massNumber of molelcules
Total (without water)15,3262
Polymers15,3262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-24 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.958, 57.554, 98.886
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Enhancer of yellow 2b transcription factor / Testis-specific e(y)2 paralog


Mass: 10846.636 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: e(y)2b, CG14612 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VI60
#2: Protein/peptide SAGA-associated factor 11 homolog


Mass: 4478.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sgf11, CG13379 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VVR6
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0; 20% isopropanol, 22% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.55→18.75 Å / Num. obs: 8047 / % possible obs: 94.6 % / Redundancy: 2.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.042 / Rrim(I) all: 0.076 / Χ2: 0.94 / Net I/σ(I): 4.9 / Num. measured all: 21826
Reflection shellResolution: 2.55→2.66 Å / % possible obs: 98.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 1.151 / Num. measured all: 2832 / Num. unique obs: 1028 / CC1/2: 0.415 / Rpim(I) all: 0.763 / Rrim(I) all: 1.387 / Χ2: 0.93 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.55→18.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.843 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26205 389 4.8 %RANDOM
Rwork0.21405 ---
obs0.21635 7656 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.134 Å2
Baniso -1Baniso -2Baniso -3
1--41.7 Å2-0 Å2-18.46 Å2
2--32.25 Å20 Å2
3---9.45 Å2
Refinement stepCycle: 1 / Resolution: 2.55→18.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 0 0 1532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121548
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161436
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.8092101
X-RAY DIFFRACTIONr_angle_other_deg1.1231.7673298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4015203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.65259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.22510251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1340.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021856
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02332
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it14.5119.874824
X-RAY DIFFRACTIONr_mcbond_other14.5089.873824
X-RAY DIFFRACTIONr_mcangle_it19.83117.8661023
X-RAY DIFFRACTIONr_mcangle_other19.82617.8691024
X-RAY DIFFRACTIONr_scbond_it14.8519.987724
X-RAY DIFFRACTIONr_scbond_other14.8429.988725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other19.86618.3661079
X-RAY DIFFRACTIONr_long_range_B_refined27.508116.255871
X-RAY DIFFRACTIONr_long_range_B_other27.508116.245872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 25 -
Rwork0.187 595 -
obs--98.1 %

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