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- PDB-4oy2: Crystal structure of TAF1-TAF7, a TFIID subcomplex -

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Basic information

Entry
Database: PDB / ID: 4oy2
TitleCrystal structure of TAF1-TAF7, a TFIID subcomplex
Components
  • Transcription initiation factor TFIID subunit 1
  • Transcription initiation factor TFIID subunit 7
KeywordsTRANSCRIPTION / TAF1 / TAF7 / TFIID / RNA Pol II initiation factors
Function / homology
Function and homology information


RNA polymerase II general transcription initiation factor binding / histone acetyltransferase binding / RNA polymerase II general transcription initiation factor activity / 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 / transcription factor TFIID complex / RNA Polymerase II Pre-transcription Events / transcription factor binding ...RNA polymerase II general transcription initiation factor binding / histone acetyltransferase binding / RNA polymerase II general transcription initiation factor activity / 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 / transcription factor TFIID complex / RNA Polymerase II Pre-transcription Events / transcription factor binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / TBP-class protein binding / transcription by RNA polymerase II / transcription coactivator activity / molecular adaptor activity / transcription cis-regulatory region binding / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591)
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsBhattacharya, S. / Lou, X. / Rajashankar, K. / Jacobson, R.H. / Webb, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK41482 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and functional insight into TAF1-TAF7, a subcomplex of transcription factor II D.
Authors: Bhattacharya, S. / Lou, X. / Hwang, P. / Rajashankar, K.R. / Wang, X. / Gustafsson, J.-A. / Fletterick, R.J. / Jacobson, R.H. / Webb, P.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Structure summary
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / symmetry
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _symmetry.Int_Tables_number
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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 1
C: Transcription initiation factor TFIID subunit 1
E: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 7
D: Transcription initiation factor TFIID subunit 7
F: Transcription initiation factor TFIID subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,6358
Polymers258,4486
Non-polymers1882
Water23413
1
A: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2153
Polymers86,1492
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-100 kcal/mol
Surface area31600 Å2
MethodPISA
2
C: Transcription initiation factor TFIID subunit 1
D: Transcription initiation factor TFIID subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2713
Polymers86,1492
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-62 kcal/mol
Surface area31700 Å2
MethodPISA
3
E: Transcription initiation factor TFIID subunit 1
F: Transcription initiation factor TFIID subunit 7


Theoretical massNumber of molelcules
Total (without water)86,1492
Polymers86,1492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-54 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.215, 123.660, 229.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription initiation factor TFIID subunit 1 / TAFII-130 / TAFII-145 / TBP-associated factor 1 / TBP-associated factor 145 kDa


Mass: 58755.855 Da / Num. of mol.: 3 / Fragment: UNP residues 455-960
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: G9374,P46677,TAF1,TAF130,TAF145,YGR274C / Plasmid: PETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46677, histone acetyltransferase
#2: Protein Transcription initiation factor TFIID subunit 7 / TAFII-67 / TBP-associated factor 67 kDa / TBP-associated factor 7


Mass: 27393.350 Da / Num. of mol.: 3 / Fragment: UNP residues 86-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: Q05021,TAF67,TAF7,YM9959.09C,YMR227C / Plasmid: PETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q05021
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.34 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 295 K / Method: evaporation / Details: 20% PEG3350, 150mM ammonium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.89→84 Å / Num. obs: 77983 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 70.59 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: SAD / Resolution: 2.9→83.676 Å / FOM work R set: 0.82 / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.41 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 3934 5.05 %
Rwork0.2087 73978 -
obs0.2105 77912 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.99 Å2 / Biso mean: 80.32 Å2 / Biso min: 30.5 Å2
Refinement stepCycle: final / Resolution: 2.9→83.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16345 0 9 13 16367
Biso mean--107.04 55.97 -
Num. residues----2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416826
X-RAY DIFFRACTIONf_angle_d0.80622812
X-RAY DIFFRACTIONf_chiral_restr0.0552510
X-RAY DIFFRACTIONf_plane_restr0.0033002
X-RAY DIFFRACTIONf_dihedral_angle_d14.426307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.93210.37611300.33242587271799
2.9321-2.96930.39321300.334226192749100
2.9693-3.00830.33481580.303125792737100
3.0083-3.04960.32191400.296726302770100
3.0496-3.09310.31561280.280426302758100
3.0931-3.13930.32571530.276825842737100
3.1393-3.18830.3311530.268626012754100
3.1883-3.24060.31141240.265226182742100
3.2406-3.29650.34831380.267626422780100
3.2965-3.35640.36821390.259526132752100
3.3564-3.4210.2681280.25426392767100
3.421-3.49080.34371500.252826002750100
3.4908-3.56670.25441460.237326122758100
3.5667-3.64970.29081610.221126122773100
3.6497-3.7410.28181300.214526362766100
3.741-3.84210.25071540.198426242778100
3.8421-3.95520.23131410.201826352776100
3.9552-4.08280.20691450.185426262771100
4.0828-4.22880.21451400.184426362776100
4.2288-4.39810.21091390.173726362775100
4.3981-4.59820.17841250.164426682793100
4.5982-4.84060.18641400.167526592799100
4.8406-5.14390.22081320.174326792811100
5.1439-5.5410.19561280.18326832811100
5.541-6.09840.21881320.196326792811100
6.0984-6.98050.22131470.197726952842100
6.9805-8.79320.18421730.179627072880100
8.7932-83.71130.2331300.20142849297999

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