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- PDB-8u77: Crystal structure of Taf14 in complex with Yng1 -

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Basic information

Entry
Database: PDB / ID: 8u77
TitleCrystal structure of Taf14 in complex with Yng1
Components
  • Protein YNG1
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION / Complex / Taf14 / Yng1 / transcription factor
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / SUMOylation of transcription cofactors / transcription factor TFIIF complex / Ino80 complex / mediator complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / SUMOylation of transcription cofactors / transcription factor TFIIF complex / Ino80 complex / mediator complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / : / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / ING family / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Zinc finger, PHD-type ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / ING family / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 14 / Protein YNG1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsNguyen, M.C. / Wei, P.C. / Zhang, G.Y. / Kutateladze, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director United States
CitationJournal: Nat Commun / Year: 2024
Title: Molecular insight into interactions between the Taf14, Yng1 and Sas3 subunits of the NuA3 complex.
Authors: Nguyen, M.C. / Rostamian, H. / Raman, A. / Wei, P. / Becht, D.C. / Erbse, A.H. / Klein, B.J. / Gilbert, T.M. / Zhang, G. / Blanco, M.A. / Strahl, B.D. / Taverna, S.D. / Kutateladze, T.G.
History
DepositionSep 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
B: Protein YNG1
C: Transcription initiation factor TFIID subunit 14
D: Protein YNG1
E: Transcription initiation factor TFIID subunit 14
F: Protein YNG1
G: Transcription initiation factor TFIID subunit 14
H: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)37,9768
Polymers37,9768
Non-polymers00
Water5,927329
1
A: Transcription initiation factor TFIID subunit 14
B: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-10 kcal/mol
Surface area5260 Å2
MethodPISA
2
C: Transcription initiation factor TFIID subunit 14
D: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area5310 Å2
MethodPISA
3
E: Transcription initiation factor TFIID subunit 14
F: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area5020 Å2
MethodPISA
4
G: Transcription initiation factor TFIID subunit 14
H: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area5060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.780, 64.610, 64.490
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 8053.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35189
#2: Protein/peptide
Protein YNG1 / ING1 homolog 1


Mass: 1440.855 Da / Num. of mol.: 4 / Fragment: UNP residues 113-124 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08465
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→45.84 Å / Num. obs: 28287 / % possible obs: 99.78 % / Redundancy: 27.2 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.04643 / Rpim(I) all: 0.04643 / Rrim(I) all: 0.06566 / Net I/σ(I): 10.92
Reflection shellResolution: 1.93→2 Å / Redundancy: 26.2 % / Rmerge(I) obs: 0.1498 / Mean I/σ(I) obs: 4.36 / Num. unique obs: 2781 / CC1/2: 0.851 / Rpim(I) all: 0.1498 / Rrim(I) all: 0.2119 / % possible all: 99.64

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→45.84 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 2000 7.08 %
Rwork0.1824 --
obs0.1852 28235 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 0 329 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052583
X-RAY DIFFRACTIONf_angle_d0.823493
X-RAY DIFFRACTIONf_dihedral_angle_d5.51324
X-RAY DIFFRACTIONf_chiral_restr0.051425
X-RAY DIFFRACTIONf_plane_restr0.004438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.28641390.21281835X-RAY DIFFRACTION99
1.98-2.030.25361440.19631881X-RAY DIFFRACTION100
2.03-2.090.22571420.18721860X-RAY DIFFRACTION100
2.09-2.160.22641420.19061865X-RAY DIFFRACTION100
2.16-2.240.22541440.17661886X-RAY DIFFRACTION100
2.24-2.330.20281430.16941871X-RAY DIFFRACTION100
2.33-2.440.20041400.17441843X-RAY DIFFRACTION100
2.44-2.560.23751430.17511882X-RAY DIFFRACTION100
2.56-2.720.20881430.18211864X-RAY DIFFRACTION100
2.72-2.930.22131450.18911904X-RAY DIFFRACTION100
2.93-3.230.22941420.19011868X-RAY DIFFRACTION100
3.23-3.70.20941440.17351879X-RAY DIFFRACTION100
3.7-4.660.20531440.16191908X-RAY DIFFRACTION100
4.66-45.840.22351450.20281889X-RAY DIFFRACTION98

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