[English] 日本語
Yorodumi
- PDB-6yj6: Structure of the TFIIIC subcomplex tauA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yj6
TitleStructure of the TFIIIC subcomplex tauA
Components
  • Transcription factor tau 131 kDa subunit
  • Transcription factor tau 55 kDa subunit
  • Transcription factor tau 95 kDa subunit,Transcription factor tau 95 kDa subunit
KeywordsTRANSCRIPTION / TFIIIC / tauA / Transcription initiation / Pol III / TFIIIB / Transcription factor
Function / homology
Function and homology information


5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / phosphatase activity / transcription by RNA polymerase III / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor TFIIIC subunit Tfc7/tau55 / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor Tfc4/TFIIIC-102/Sfc4 / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain / TFIIIC, subcomplex tauA subunit Sfc1, triple barrel domain superfamily / RNA polymerase III transcription factor (TF)IIIC subunit HTH domain / TFIIIC subunit triple barrel domain / Tau95 Triple barrel domain ...Transcription factor TFIIIC subunit Tfc7/tau55 / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor Tfc4/TFIIIC-102/Sfc4 / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain / TFIIIC, subcomplex tauA subunit Sfc1, triple barrel domain superfamily / RNA polymerase III transcription factor (TF)IIIC subunit HTH domain / TFIIIC subunit triple barrel domain / Tau95 Triple barrel domain / Tetratricopeptide repeat / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Tetratricopeptide repeat / Histidine phosphatase superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Transcription factor tau 95 kDa subunit / Transcription factor tau 131 kDa subunit / Transcription factor tau 55 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVorlaender, M.K. / Muller, C.W.
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the TFIIIC subcomplex τA provides insights into RNA polymerase III pre-initiation complex formation.
Authors: Matthias K Vorländer / Anna Jungblut / Kai Karius / Florence Baudin / Helga Grötsch / Jan Kosinski / Christoph W Müller /
Abstract: Transcription factor (TF) IIIC is a conserved eukaryotic six-subunit protein complex with dual function. It serves as a general TF for most RNA polymerase (Pol) III genes by recruiting TFIIIB, but it ...Transcription factor (TF) IIIC is a conserved eukaryotic six-subunit protein complex with dual function. It serves as a general TF for most RNA polymerase (Pol) III genes by recruiting TFIIIB, but it is also involved in chromatin organization and regulation of Pol II genes through interaction with CTCF and condensin II. Here, we report the structure of the S. cerevisiae TFIIIC subcomplex τA, which contains the most conserved subunits of TFIIIC and is responsible for recruitment of TFIIIB and transcription start site (TSS) selection at Pol III genes. We show that τA binding to its promoter is auto-inhibited by a disordered acidic tail of subunit τ95. We further provide a negative-stain reconstruction of τA bound to the TFIIIB subunits Brf1 and TBP. This shows that a ruler element in τA achieves positioning of TFIIIB upstream of the TSS, and suggests remodeling of the complex during assembly of TFIIIB by TFIIIC.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10817
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription factor tau 131 kDa subunit
B: Transcription factor tau 95 kDa subunit,Transcription factor tau 95 kDa subunit
C: Transcription factor tau 55 kDa subunit


Theoretical massNumber of molelcules
Total (without water)247,3103
Polymers247,3103
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19590 Å2
ΔGint-102 kcal/mol
Surface area74610 Å2
MethodPISA

-
Components

#1: Protein Transcription factor tau 131 kDa subunit / TFIIIC 131 kDa subunit / Transcription factor C subunit 4


Mass: 120746.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC4, PCF1, YGR047C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33339
#2: Protein Transcription factor tau 95 kDa subunit,Transcription factor tau 95 kDa subunit / TFIIIC 95 kDa subunit / Transcription factor C subunit 1


Mass: 77363.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC1, YBR123C, YBR0919 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32367
#3: Protein Transcription factor tau 55 kDa subunit / TFIIIC 55 kDa subunit / Transcription factor C subunit 7


Mass: 49198.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TFC7, YOR110W, O3234, YOR3234w / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12415

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: TFIIIC subcomplex tauA / Type: COMPLEX
Details: Generated by co-expression of subunits in insect cells
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.245 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Strain: Hi 5 cells
Buffer solutionpH: 7.5 / Details: 20 mM HEPES, 5 mM DTT, 75 mM NaCl
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 4 mM CHAPSO added prior to freezing
Specimen supportDetails: Pelco Easygglow instrument / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot force 2, Blot time 4

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: -2000 nm / Nominal defocus min: -500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 48.73 sec. / Electron dose: 1.35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5824 / Details: collected 8 frames per hole using beam shift
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 36 / Used frames/image: 1-36

-
Processing

EM software
IDNameVersionCategory
1Warp1.06particle selection
2SerialEM3.7 betaimage acquisition
4Warp1.06CTF correction
7Coot0.9 pre-releasemodel fitting
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 702583 / Details: BoxNet2_20180918 was used for particle picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254700 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

+
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://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