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- PDB-2p6v: Structure of TAFH domain of the human TAF4 subunit of TFIID -

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Basic information

Entry
Database: PDB / ID: 2p6v
TitleStructure of TAFH domain of the human TAF4 subunit of TFIID
ComponentsTranscription initiation factor TFIID subunit 4
KeywordsTRANSCRIPTION / ALPHA HELIX
Function / homology
Function and homology information


transcription factor TFTC complex / transcription factor TFIID complex / 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 / MLL1 complex ...transcription factor TFTC complex / transcription factor TFIID complex / 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 / MLL1 complex / aryl hydrocarbon receptor binding / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / ovarian follicle development / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
TAFH/NHR1 domain / Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...TAFH/NHR1 domain / Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histone-fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWang, X. / Truckses, D.M. / Takada, S. / Matsumura, T. / Tanese, N. / Jacobson, R.H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Conserved region I of human coactivator TAF4 binds to a short hydrophobic motif present in transcriptional regulators.
Authors: Wang, X. / Truckses, D.M. / Takada, S. / Matsumura, T. / Tanese, N. / Jacobson, R.H.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7472
Polymers12,6511
Non-polymers961
Water70339
1
A: Transcription initiation factor TFIID subunit 4
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)76,48412
Polymers75,9086
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
crystal symmetry operation11_656-x+y+1,y,-z+3/21
crystal symmetry operation12_556x,x-y,-z+3/21
Unit cell
Length a, b, c (Å)74.852, 74.852, 131.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-700-

SO4

21A-31-

HOH

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Components

#1: Protein Transcription initiation factor TFIID subunit 4 / TBP-associated factor 4 / Transcription initiation factor TFIID 135 kDa subunit / TAFII / 135 / ...TBP-associated factor 4 / Transcription initiation factor TFIID 135 kDa subunit / TAFII / 135 / TAFII-135 / TAFII135 / TAFII-130 / TAFII130


Mass: 12651.351 Da / Num. of mol.: 1 / Fragment: TAFH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF4, TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: O00268
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Crystals of methylated hTAF4-TAFH containing SeMet were grown by hanging drop vapor diffusion at 22 C by mixing equal volumes of protein solution and crystallization buffer (200 mM ammonium ...Details: Crystals of methylated hTAF4-TAFH containing SeMet were grown by hanging drop vapor diffusion at 22 C by mixing equal volumes of protein solution and crystallization buffer (200 mM ammonium acetate, 2.2 M ammonium sulfate and 150 mM sodium bromide). , pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9797, 1.0199
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
21.01991
ReflectionResolution: 2→65.94 Å / Num. all: 15659 / Num. obs: 15423 / % possible obs: 98.49 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.107 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2184 / Rsym value: 0.11 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2→65.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.843 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24835 786 5.2 %RANDOM
Rwork0.21402 ---
all0.214 15659 --
obs0.21567 15423 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.387 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å21.36 Å20 Å2
2--2.71 Å20 Å2
3----4.07 Å2
Refinement stepCycle: LAST / Resolution: 2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms776 0 5 39 820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021790
X-RAY DIFFRACTIONr_bond_other_d0.0010.02762
X-RAY DIFFRACTIONr_angle_refined_deg2.3432.0561069
X-RAY DIFFRACTIONr_angle_other_deg1.16731774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.569596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87225.15233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6915116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.37155
X-RAY DIFFRACTIONr_chiral_restr0.1190.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02834
X-RAY DIFFRACTIONr_gen_planes_other00.02139
X-RAY DIFFRACTIONr_nbd_refined0.2420.3199
X-RAY DIFFRACTIONr_nbd_other0.220.3793
X-RAY DIFFRACTIONr_nbtor_refined0.2130.5391
X-RAY DIFFRACTIONr_nbtor_other0.1680.5493
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.557
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4330.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.175607
X-RAY DIFFRACTIONr_mcbond_other7.5645193
X-RAY DIFFRACTIONr_mcangle_it12.6613790
X-RAY DIFFRACTIONr_scbond_it16.1834324
X-RAY DIFFRACTIONr_scangle_it17.2672279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 50 -
Rwork0.342 1018 -
obs--98.34 %

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