[English] 日本語
Yorodumi
- PDB-6e16: Ternary structure of c-Myc-TBP-TAF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling / TFIIA-class transcription factor complex binding ...SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling / TFIIA-class transcription factor complex binding / TFAP2 (AP-2) family regulates transcription of cell cycle factors / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / 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 / transcription regulator activator activity / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / RNA polymerase II general transcription initiation factor binding / regulation of telomere maintenance / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / DNA binding, bending / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / negative regulation of gene expression via chromosomal CpG island methylation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / branching involved in ureteric bud morphogenesis / RNA polymerase II transcribes snRNA genes / Signaling by ALK / 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 / RNA Polymerase I Promoter Escape / E-box binding / nucleolar large rRNA transcription by RNA polymerase I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Estrogen-dependent gene expression / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / chromosome organization / RNA polymerase II core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / : / ERK1 and ERK2 cascade / TBP-class protein binding / DNA-templated transcription initiation / transcription coregulator binding / positive regulation of epithelial cell proliferation / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / cellular response to UV / MAPK cascade / positive regulation of fibroblast proliferation / disordered domain specific binding / cellular response to xenobiotic stimulus / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / intracellular iron ion homeostasis / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / molecular adaptor activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / chromatin remodeling / response to xenobiotic stimulus / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding
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 / Protein of unknown function (DUF3591) ...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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more