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- PDB-7uhe: Taf14 ET domain in complex with C-terminal tail of Taf2 -

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Basic information

Entry
Database: PDB / ID: 7uhe
TitleTaf14 ET domain in complex with C-terminal tail of Taf2
Components
  • C-terminal tail of Transcription initiation factor TFIID subunit 2
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION / AHD / Preinitiation complex (PIC) / Chromatin-modification / DNA-binding
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / transcription factor TFIIF complex / mediator complex / SWI/SNF complex / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / transcription factor TFIIF complex / mediator complex / SWI/SNF complex / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / histone binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / Transcription initiation factor TFIID subunit 2 / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / NET domain / Bromodomain extra-terminal - transcription regulation
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 14
Similarity search - Component
Biological speciesSaccharomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsKlein, B.J. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Taf2 mediates DNA binding of Taf14.
Authors: Klein, B.J. / Feigerle, J.T. / Zhang, J. / Ebmeier, C.C. / Fan, L. / Singh, R.K. / Wang, W.W. / Schmitt, L.R. / Lee, T. / Hansen, K.C. / Liu, W.R. / Wang, Y.X. / Strahl, B.D. / Anthony Weil, ...Authors: Klein, B.J. / Feigerle, J.T. / Zhang, J. / Ebmeier, C.C. / Fan, L. / Singh, R.K. / Wang, W.W. / Schmitt, L.R. / Lee, T. / Hansen, K.C. / Liu, W.R. / Wang, Y.X. / Strahl, B.D. / Anthony Weil, P. / Kutateladze, T.G.
History
DepositionMar 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Transcription initiation factor TFIID subunit 14
B: C-terminal tail of Transcription initiation factor TFIID subunit 2
C: Transcription initiation factor TFIID subunit 14
D: C-terminal tail of Transcription initiation factor TFIID subunit 2


Theoretical massNumber of molelcules
Total (without water)19,6804
Polymers19,6804
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, HSQC NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.889, 52.714, 121.507
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
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-359-

HOH

31A-364-

HOH

41B-1505-

HOH

51C-363-

HOH

61C-368-

HOH

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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: 8369.418 Da / Num. of mol.: 2 / Fragment: ET domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces (fungus) / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia (bacteria) / References: UniProt: P35189
#2: Protein/peptide C-terminal tail of Transcription initiation factor TFIID subunit 2 / TAFII-150 / TBP-associated factor 150 kDa / TBP-associated factor 2 / TSM-1


Mass: 1470.783 Da / Num. of mol.: 2 / Fragment: C-terminal tail / Source method: obtained synthetically / Source: (synth.) Saccharomyces (fungus) / References: UniProt: P23255
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate

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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: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 18278 / % possible obs: 98.2 % / Redundancy: 9.6 % / Biso Wilson estimate: 20.55 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.027 / Net I/σ(I): 48.5
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2.5 % / Num. unique obs: 734 / CC1/2: 0.943 / Rpim(I) all: 0.108

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LQZ

6lqz


Resolution: 1.66→35.45 Å / SU ML: 0.2081 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.6618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 1806 9.98 %
Rwork0.1905 16288 -
obs0.1948 18094 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.2 Å2
Refinement stepCycle: LAST / Resolution: 1.66→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 0 157 1453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651310
X-RAY DIFFRACTIONf_angle_d0.86531765
X-RAY DIFFRACTIONf_chiral_restr0.0566213
X-RAY DIFFRACTIONf_plane_restr0.0086220
X-RAY DIFFRACTIONf_dihedral_angle_d15.599493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.710.27521070.2201998X-RAY DIFFRACTION78.09
1.71-1.760.27541350.21441188X-RAY DIFFRACTION94.64
1.76-1.810.27521370.22751237X-RAY DIFFRACTION98.28
1.81-1.880.29171400.20741284X-RAY DIFFRACTION99.03
1.88-1.950.27631380.20521237X-RAY DIFFRACTION99.35
1.95-2.040.23491380.19151260X-RAY DIFFRACTION99.29
2.04-2.150.25951420.18391272X-RAY DIFFRACTION99.86
2.15-2.280.22271410.1951273X-RAY DIFFRACTION99.86
2.28-2.460.23981420.19021276X-RAY DIFFRACTION99.72
2.46-2.710.26941460.20631299X-RAY DIFFRACTION99.79
2.71-3.10.25011420.20081283X-RAY DIFFRACTION99.79
3.1-3.90.19231460.17571318X-RAY DIFFRACTION99.59
3.9-35.450.21261520.17621363X-RAY DIFFRACTION98.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.073552100970.5455043948270.4160888448570.3341708165470.2768267779151.08438891309-0.229784966502-0.2562925152040.1334666895570.03246862495130.246735699828-0.182333708868-0.18559641521-0.1799847467450.008274068031920.130903046322-0.00771230563074-0.02590198040680.175202756268-0.01392485085020.2019429727385.38928.19547.9
20.229635617792-0.083067902653-0.01205541467320.6366125402750.1462357758210.3887891383330.11572392259-0.192018431858-0.1482302197710.173714177944-0.0580470381820.1517599154680.42425992671-0.332781909032-0.00694123220070.254578147621-0.007419097176440.01838440568990.1756969693580.03568645083330.207741130031-2.40417.445.335
31.776729434930.8696631933120.4504687075681.856437551831.768257156861.97810749179-0.01030992928840.5109918545040.00368320007038-0.01319035268760.2358840183590.122638419037-0.121575185826-0.705055421221.076283229870.1517107908260.04381635067120.004062303900090.2540575401270.0495206057420.137382084549-4.72823.5333.234
41.243135420810.033180516590.0234149320380.51740048261-0.09881788325270.0206638183862-0.6994642627330.130269860733-0.494033834426-1.083935963020.061677901021-0.087540391530.4340271972610.413966763073-0.1772849022110.4029701863960.06684821582410.04549395608390.2512477591730.06375441708630.3240343695326.38811.57335.804
50.3273550563580.1073569922970.04813962304660.1486021064440.04071003841980.0917904928224-0.121469474197-0.245768295464-0.06792848378060.02523267474310.252156211983-0.101930279221-0.0980622250126-0.0745110748517-9.90399362509E-60.1802783986530.013594055854-0.01939492390440.1850148179490.02471644250290.1632310539360.13726.75338.057
60.3916531400290.02420814995160.09247668032930.6068915999430.103604040220.509277421233-0.100222235971-0.487002493060.1382648984590.1486140959420.1020954956120.08027035378260.0449776917718-0.3048691850090.01229596838040.1909192253550.04574890301550.003390064901840.240292535106-0.02947029922520.174066986335-1.69826.54351.307
70.5822017447620.5866715452210.01228876428320.63283933840.3335815463110.3177068468060.05358256256740.129012365823-0.220079280372-0.126496738336-0.157330535223-0.2246996820530.1344820525750.6507760456170.00242356716030.2838581924250.0286309201088-0.06544563170380.2366627995950.02326279959470.2430038377437.73323.95137.918
81.083355486450.528564586828-0.484775937681.53272878051-0.181824070311.101973323880.0845844758294-0.1176747852910.151326221584-0.0634499505680.1444094797460.196901441181-0.03456133736640.01611025029570.1041877040990.1659238955430.001653906735740.05257040130490.1313716049940.02111141187670.25158803056227.40132.6844.109
90.1870782360120.002953592035480.1992152263110.447122877330.1051695903790.323152978844-0.0349799178356-0.205879704439-0.131046724789-0.1837162394240.125589090037-0.03107245678950.2131970840080.055987539113-8.97445571523E-50.183224963738-0.024237342319-0.03866527549760.2080773803040.009734571514080.20823388350116.68223.93145.641
100.7116358545190.8801313183930.7709006962121.158628192511.140066824151.36124738808-0.1210053159450.02560908665730.00570145668113-0.180186590085-0.02872761609510.05433067519980.00360248336147-0.126005151183-0.09119063829580.1619312472860.0139483217389-0.0346803161250.177260079080.0198288389790.1597148833620.1527.42454.951
110.4798876890180.102743431491-0.1124098286780.348757474677-0.3923582307540.4554992541010.02942085440120.324364260059-0.0664136550893-0.1342426991570.097953955534-0.02577925096830.133165280458-0.3154504325610.02478719130780.2259980986610.03835613450780.01961575750670.1960163282240.005880953335840.1620800021625.98125.50640.018
120.9997107519840.227260503101-0.9006257494612.015866476290.3559823518030.967141553267-0.04817001768140.09371987733270.277450518737-0.2485049368920.100220020814-0.037194415033-0.01889679711940.2201098338250.190103111540.2514224421-0.0332567296254-0.01440773983780.2183398547170.06876967110710.18451953591323.87434.13553.662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 172:189 )A172 - 189
2X-RAY DIFFRACTION2( CHAIN A AND RESID 190:203 )A190 - 203
3X-RAY DIFFRACTION3( CHAIN A AND RESID 204:209 )A204 - 209
4X-RAY DIFFRACTION4( CHAIN A AND RESID 210:217 )A210 - 217
5X-RAY DIFFRACTION5( CHAIN A AND RESID 218:227 )A218 - 227
6X-RAY DIFFRACTION6( CHAIN A AND RESID 228:241 )A228 - 241
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1393:1401 )B1393 - 1401
8X-RAY DIFFRACTION8( CHAIN C AND RESID 170:189 )C170 - 189
9X-RAY DIFFRACTION9( CHAIN C AND RESID 190:203 )C190 - 203
10X-RAY DIFFRACTION10( CHAIN C AND RESID 204:227 )C204 - 227
11X-RAY DIFFRACTION11( CHAIN C AND RESID 228:241 )C228 - 241
12X-RAY DIFFRACTION12( CHAIN D AND RESID 1392:1401 )D1392 - 1401

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