[English] 日本語
Yorodumi
- EMDB-5134: TBP-containing S. pombe TFIID -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5134
TitleTBP-containing S. pombe TFIID
Map dataTBP-containing S. pombe TFIID
Sample
  • Sample: Native S. pombe TFIID
  • Protein or peptide: TAF1-TAF12, TBP
Function / homologyTranscription initiation factor TFIID subunit 12 domain / transcription factor TFIID complex
Function and homology information
Biological speciesS. pombe
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsElmlund H / Baraznenok V / Linder T / Szilagyi Z / Rofougaran R / Hofer A / Hebert H / Lindahl M / Gustafsson CM
CitationJournal: Structure / Year: 2009
Title: Cryo-EM reveals promoter DNA binding and conformational flexibility of the general transcription factor TFIID.
Authors: Hans Elmlund / Vera Baraznenok / Tomas Linder / Zsolt Szilagyi / Reza Rofougaran / Anders Hofer / Hans Hebert / Martin Lindahl / Claes M Gustafsson /
Abstract: The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and ...The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and several conserved TBP-associated factors (TAFs). Recognition of the core promoter by TFIID assists assembly of the preinitiation complex. Using cryo-electron microscopy in combination with methods for ab initio single-particle reconstruction and heterogeneity analysis, we have produced density maps of two conformational states of Schizosaccharomyces pombe TFIID, containing and lacking TBP. We report that TBP-binding is coupled to a massive histone-fold domain rearrangement. Moreover, docking of the TBP-TAF1(N-terminus) atomic structure to the TFIID map and reconstruction of a TAF-promoter DNA complex helps to account for TAF-dependent regulation of promoter-TBP and promoter-TAF interactions.
History
DepositionOct 19, 2009-
Header (metadata) releaseNov 2, 2009-
Map releaseNov 2, 2009-
UpdateJan 10, 2011-
Current statusJan 10, 2011Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0008
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5134.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTBP-containing S. pombe TFIID
Voxel sizeX=Y=Z: 2.33 Å
Density
Contour LevelBy AUTHOR: 0.001 / Movie #1: 0.0008
Minimum - Maximum-0.00751961 - 0.0496766
Average (Standard dev.)0.000273146 (±0.00203491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 233 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z233.000233.000233.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.0080.0500.000

-
Supplemental data

-
Sample components

-
Entire : Native S. pombe TFIID

EntireName: Native S. pombe TFIID
Components
  • Sample: Native S. pombe TFIID
  • Protein or peptide: TAF1-TAF12, TBP

-
Supramolecule #1000: Native S. pombe TFIID

SupramoleculeName: Native S. pombe TFIID / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 870 KDa / Theoretical: 870 KDa / Method: GEMMA

-
Macromolecule #1: TAF1-TAF12, TBP

MacromoleculeName: TAF1-TAF12, TBP / type: protein_or_peptide / ID: 1 / Name.synonym: TFIID / Recombinant expression: No / Database: NCBI
Source (natural)Organism: S. pombe / synonym: Fission yeast
SequenceGO: transcription factor TFIID complex
InterPro: Transcription initiation factor TFIID subunit 12 domain

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SIMPLE

+
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