[English] 日本語
Yorodumi
- EMDB-5176: Frozen hydrated map of the yeast TFIID-TFIIA-Rap1-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5176
TitleFrozen hydrated map of the yeast TFIID-TFIIA-Rap1-DNA complex
Map dataYeast TFIID in complex with Rap1 and DNA
Sample
  • Sample: HA-tag purified yeast TFIID
  • Protein or peptide: Rap1
  • Protein or peptide: TFIID
KeywordsTranscription / general transcription factor / TFIID / transcription initiation / transciption activator / TFIIA / Rap1
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.5 Å
AuthorsPapai G / Tripathi MK / Ruhlmann C / Layer JH / Weil PA / Schultz P
CitationJournal: Nature / Year: 2010
Title: TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation.
Authors: Gabor Papai / Manish K Tripathi / Christine Ruhlmann / Justin H Layer / P Anthony Weil / Patrick Schultz /
Abstract: Transcription of eukaryotic messenger RNA (mRNA) encoding genes by RNA polymerase II (Pol II) is triggered by the binding of transactivating proteins to enhancer DNA, which stimulates the recruitment ...Transcription of eukaryotic messenger RNA (mRNA) encoding genes by RNA polymerase II (Pol II) is triggered by the binding of transactivating proteins to enhancer DNA, which stimulates the recruitment of general transcription factors (TFIIA, B, D, E, F, H) and Pol II on the cis-linked promoter, leading to pre-initiation complex formation and transcription. In TFIID-dependent activation pathways, this general transcription factor containing TATA-box-binding protein is first recruited on the promoter through interaction with activators and cooperates with TFIIA to form a committed pre-initiation complex. However, neither the mechanisms by which activation signals are communicated between these factors nor the structural organization of the activated pre-initiation complex are known. Here we used cryo-electron microscopy to determine the architecture of nucleoprotein complexes composed of TFIID, TFIIA, the transcriptional activator Rap1 and yeast enhancer-promoter DNA. These structures revealed the mode of binding of Rap1 and TFIIA to TFIID, as well as a reorganization of TFIIA induced by its interaction with Rap1. We propose that this change in position increases the exposure of TATA-box-binding protein within TFIID, consequently enhancing its ability to interact with the promoter. A large Rap1-dependent DNA loop forms between the activator-binding site and the proximal promoter region. This loop is topologically locked by a TFIIA-Rap1 protein bridge that folds over the DNA. These results highlight the role of TFIIA in transcriptional activation, define a molecular mechanism for enhancer-promoter communication and provide structural insights into the pathways of intramolecular communication that convey transcription activation signals through the TFIID complex.
History
DepositionMar 26, 2010-
Header (metadata) releaseApr 14, 2010-
Map releaseJun 21, 2010-
UpdateJun 21, 2010-
Current statusJun 21, 2010Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5176.png

Downloads & links

-
Map

FileDownload / File: emd_5176.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast TFIID in complex with Rap1 and DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 160 pix.
= 416. Å		2.6 Å/pix.
x 160 pix.
= 416. Å		2.6 Å/pix.
x 160 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-16.079799999999999 - 54.1081
Average (Standard dev.)-0.000000000139934 (±2.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-79-80
Dimensions160160160
Spacing160160160
CellA=B=C: 416 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-79-80-80
NC/NR/NS160160160
D min/max/mean-16.08054.108-0.000

-
Supplemental data

-
Sample components

-
Entire : HA-tag purified yeast TFIID

EntireName: HA-tag purified yeast TFIID
Components
  • Sample: HA-tag purified yeast TFIID
  • Protein or peptide: Rap1
  • Protein or peptide: TFIID

-
Supramolecule #1000: HA-tag purified yeast TFIID

SupramoleculeName: HA-tag purified yeast TFIID / type: sample / ID: 1000 / Number unique components: 3
Molecular weightExperimental: 1 MDa

-
Macromolecule #1: Rap1

MacromoleculeName: Rap1 / type: protein_or_peptide / ID: 1 / Name.synonym: Rap1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Organelle: Nucleus / Location in cell: Nucleus

-
Macromolecule #2: TFIID

MacromoleculeName: TFIID / type: protein_or_peptide / ID: 2 / Name.synonym: TFIID / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Organelle: Nucleus / Location in cell: Nucleus

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.165 mg/mL
BufferpH: 7.9 / Details: 10 mM Tris-HCl pH 7.9, 300 mM KOAc and 5 mM MgCl2
GridDetails: 300 mesh Cu/Rh holey grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 80 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

-
Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 81 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5.1 µm / Number real images: 90 / Average electron dose: 16 e/Å2 / Od range: 1.4
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38950 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 39000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.5 Å / Resolution method: OTHER / Software - Name: Imagic, Spider
Details: The map was reconstructed from 3-D MSA separated dataset.
Number images used: 26901

+
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