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- PDB-6e16: Ternary structure of c-Myc-TBP-TAF1 -

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Entry
Database: PDB / ID: 6.0E+16
TitleTernary structure of c-Myc-TBP-TAF1
ComponentsTranscription initiation factor TFIID subunit 1,Myc proto-oncogene protein,TATA-box-binding protein
KeywordsDNA BINDING PROTEIN / transcriptional regulation / carcinogenesis
Function / homology
Function and homology information


positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / Myc-Max complex / negative regulation of transcription initiation by RNA polymerase II / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors ...positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / Myc-Max complex / negative regulation of transcription initiation by RNA polymerase II / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / negative regulation of cell division / RNA polymerase I general transcription initiation factor binding / negative regulation of monocyte differentiation / regulation of transcription by RNA polymerase III / response to growth factor / transcription regulator activator activity / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / regulation of telomere maintenance / DNA binding, bending / positive regulation of mesenchymal cell proliferation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Signaling by ALK / branching involved in ureteric bud morphogenesis / RNA polymerase II transcribes snRNA genes / 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 general transcription initiation factor activity / transcription factor TFIID complex / negative regulation of gene expression via chromosomal CpG island methylation / RNA Polymerase II Pre-transcription Events / rRNA metabolic process / histone acetyltransferase activity / RNA Polymerase I Promoter Escape / E-box binding / nucleolar large rRNA transcription by RNA polymerase I / positive regulation of telomere maintenance / Estrogen-dependent gene expression / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / chromosome organization / core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Cyclin A:Cdk2-associated events at S phase entry / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / negative regulation of fibroblast proliferation / TBP-class protein binding / ERK1 and ERK2 cascade / transcription coregulator binding / positive regulation of epithelial cell proliferation / DNA-templated transcription initiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / disordered domain specific binding / cellular response to UV / MAPK cascade / cellular response to xenobiotic stimulus / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / molecular adaptor activity / cellular response to hypoxia
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal 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) / Helix-loop-helix DNA-binding domain / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
Myc proto-oncogene protein / TATA-box-binding protein / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWei, Y. / Dong, A. / Sunnerhagen, M. / Penn, L. / Tong, Y. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Multiple direct interactions of TBP with the MYC oncoprotein.
Authors: Wei, Y. / Resetca, D. / Li, Z. / Johansson-Akhe, I. / Ahlner, A. / Helander, S. / Wallenhammar, A. / Morad, V. / Raught, B. / Wallner, B. / Kokubo, T. / Tong, Y. / Penn, L.Z. / Sunnerhagen, M.
History
DepositionJul 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1,Myc proto-oncogene protein,TATA-box-binding protein


Theoretical massNumber of molelcules
Total (without water)28,5101
Polymers28,5101
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.816, 72.816, 78.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Transcription initiation factor TFIID subunit 1,Myc proto-oncogene protein,TATA-box-binding protein / TAFII-130 / TAFII-145 / TBP-associated factor 1 / TBP-associated factor 145 kDa / Class E basic ...TAFII-130 / TAFII-145 / TBP-associated factor 1 / TBP-associated factor 145 kDa / Class E basic helix-loop-helix protein 39 / bHLHe39 / Proto-oncogene c-Myc / Transcription factor p64 / TATA sequence-binding protein / TBP / TATA-binding factor / TATA-box factor / Transcription factor D / Transcription initiation factor TFIID TBP subunit


Mass: 28509.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Gene: TAF1, TAF130, TAF145, YGR274C, G9374, MYC, BHLHE39, SPT15, BTF1, TBP1, YER148W
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P46677, UniProt: P01106, UniProt: P13393, histone acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.66 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 291 K / Method: batch mode
Details: 20% (w/w) PEG8000, 0.2M ammonium sulfare, and 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→36.408 Å / Num. obs: 16091 / % possible obs: 99.4 % / Redundancy: 3.7 % / Net I/σ(I): 13.75
Reflection shellResolution: 2.4→2.51 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 40BA

40ba


Resolution: 2.4→36.408 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.63
RfactorNum. reflection% reflection
Rfree0.2199 732 4.55 %
Rwork0.1767 --
obs0.1785 16090 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.73 Å2 / Biso mean: 56.2219 Å2 / Biso min: 28.38 Å2
Refinement stepCycle: final / Resolution: 2.4→36.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 0 15 1693
Biso mean---54.67 -
Num. residues----226
Refinement TLS params.Method: refined / Origin x: 100.4981 Å / Origin y: 76.6317 Å / Origin z: -11.1363 Å
111213212223313233
T0.336 Å2-0.0008 Å20.0183 Å2-0.3466 Å2-0.0059 Å2--0.3772 Å2
L2.9057 °2-0.7013 °22.4488 °2-0.7964 °2-1.1539 °2--4.6039 °2
S-0.0254 Å °0.2033 Å °0.0702 Å °0.0893 Å °-0.071 Å °-0.0583 Å °-0.1734 Å °0.3934 Å °0.0758 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 440
2X-RAY DIFFRACTION1allW1 - 16

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