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- PDB-4wv4: Heterodimer of TAF8/TAF10 -

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Basic information

Entry
Database: PDB / ID: 4wv4
TitleHeterodimer of TAF8/TAF10
Components
  • Transcription initiation factor TFIID subunit 10
  • Transcription initiation factor TFIID subunit 8
KeywordsTRANSCRIPTION / TBP-associated factor / Heterodimer / Histone fold domain
Function / homology
Function and homology information


SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / transcription factor TFTC complex / hepatocyte differentiation / maintenance of protein location in nucleus / SAGA complex / RNA polymerase binding / limb development ...SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / transcription factor TFTC complex / hepatocyte differentiation / maintenance of protein location in nucleus / SAGA complex / RNA polymerase binding / limb development / transcription preinitiation complex / regulation of fat cell differentiation / inner cell mass cell proliferation / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / regulation of RNA splicing / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / regulation of DNA repair / somitogenesis / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / male germ cell nucleus / nuclear estrogen receptor binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / G1/S transition of mitotic cell cycle / multicellular organism growth / mRNA transcription by RNA polymerase II / HATs acetylate histones / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / cell differentiation / Ub-specific processing proteases / chromatin remodeling / protein heterodimerization activity / apoptotic process / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Histone, subunit A / Histone, subunit A ...Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.909 Å
AuthorsTrowitzsch, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Commission (EC) Research Executive Agency (REA)254671 France
CitationJournal: Nat Commun / Year: 2015
Title: Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules.
Authors: Trowitzsch, S. / Viola, C. / Scheer, E. / Conic, S. / Chavant, V. / Fournier, M. / Papai, G. / Ebong, I.O. / Schaffitzel, C. / Zou, J. / Haffke, M. / Rappsilber, J. / Robinson, C.V. / ...Authors: Trowitzsch, S. / Viola, C. / Scheer, E. / Conic, S. / Chavant, V. / Fournier, M. / Papai, G. / Ebong, I.O. / Schaffitzel, C. / Zou, J. / Haffke, M. / Rappsilber, J. / Robinson, C.V. / Schultz, P. / Tora, L. / Berger, I.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: 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 10
B: Transcription initiation factor TFIID subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1714
Polymers22,0432
Non-polymers1282
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-59 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.320, 51.320, 144.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

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Components

#1: Protein Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAFII30 / TAF10


Mass: 11219.706 Da / Num. of mol.: 1 / Fragment: UNP 112-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF10, TAF2A, TAF2H, TAFII30 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12962
#2: Protein Transcription initiation factor TFIID subunit 8 / Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription ...Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription initiation factor TFIID 43 kDa subunit / hTAFII43 / TAF8


Mass: 10823.312 Da / Num. of mol.: 1 / Fragment: UNP residues 25-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF8, TAFII43, TBN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7Z7C8
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.909→44.444 Å / Num. obs: 16793 / % possible obs: 93.91 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.0292 / Net I/σ(I): 23.4
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.8798 / Mean I/σ(I) obs: 1.68 / % possible all: 58.53

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.909→44.444 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 852 5.07 %
Rwork0.2048 --
obs0.2064 16793 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.909→44.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 7 63 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031430
X-RAY DIFFRACTIONf_angle_d0.6811935
X-RAY DIFFRACTIONf_dihedral_angle_d12.077533
X-RAY DIFFRACTIONf_chiral_restr0.025232
X-RAY DIFFRACTIONf_plane_restr0.004243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.909-2.02860.33821220.3092005X-RAY DIFFRACTION73
2.0286-2.18520.32681420.26082684X-RAY DIFFRACTION97
2.1852-2.40510.27121470.23672733X-RAY DIFFRACTION98
2.4051-2.75310.25241470.22232754X-RAY DIFFRACTION98
2.7531-3.46840.26381510.22162805X-RAY DIFFRACTION98
3.4684-44.45650.19061430.17132960X-RAY DIFFRACTION98
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)
19.78791.7545-1.73764.04212.35062.21140.7271-0.93110.77272.3932-0.0847-0.5785-1.59330.3567-0.49660.98890.05270.07580.5671-0.11230.473115.1620.058324.653
28.77212.48273.80997.49616.04295.28330.8872-0.34170.86411.1964-0.5242-0.6727-1.32790.7687-0.52580.7425-0.21960.16650.4849-0.01640.575718.37471.998911.2004
34.56610.5286-1.77151.2490.04514.2910.14710.71880.1129-0.12320.52690.056-0.5081-0.92280.43840.31490.36980.42680.7580.25430.35426.4822-0.17852.9093
42.52050.89471.730.48670.30211.7648-0.10660.39690.75040.16820.29080.6464-1.0663-0.47450.58640.80720.41250.25130.67330.3210.53441.56722.515210.6283
54.7453-1.363-2.79683.56550.7575.16060.04280.1799-0.18590.36160.5557-0.6122-0.20930.4444-0.44860.38140.15120.01150.3358-0.11540.441516.8943-10.264510.6807
63.2362-1.3976-2.07762.5479-1.57014.4734-0.4903-0.2324-0.9740.38010.3494-1.35580.79230.8039-0.39460.54480.28240.00240.7657-0.40291.111530.3071-22.40643.1686
73.6406-1.07822.38185.43550.12523.6263-0.2638-0.4242-0.37120.84680.56790.19930.13310.1594-0.23170.55420.18790.13420.4603-0.14840.604412.2437-24.08174.044
88.9003-2.77970.97598.1918-2.69566.6510.00531.32890.262-0.51360.2619-0.3578-0.0058-0.5075-0.23790.2481-0.00030.11090.7153-0.09720.40818.239-4.1451-2.0528
95.7656-1.3371-1.00174.79520.08654.06960.09360.7661-0.34390.12130.21640.3001-0.4853-0.9372-0.11320.30020.18020.06410.49350.03670.29077.9773-8.50286.8386
100.4824-1.16640.4754.47330.58226.76010.07710.2347-0.14540.81180.4743-0.6914-0.19470.8946-0.4720.43150.1579-0.01630.4632-0.08960.437315.0279-6.877116.5249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 113 through 124 )
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 131 )
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 148 )
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 196 )
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 212 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 48 )
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 89 )
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 120 )

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