[English] 日本語
Yorodumi
- EMDB-1196: Cryo-electron microscopy studies of human TFIID: conformational b... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1196
TitleCryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.
Map data3D reconstruction of human TFIID in solution (cryo-E.M.), group 2
SampleHuman TFIIDTranscription factor II D:
TFIIDTranscription factor II D
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 35 Å resolution
AuthorsGrob P / Cruse MJ / Inouye C / Peris M / Penczek PA / Tjian R / Nogales E
CitationJournal: Structure / Year: 2006
Title: Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.
Authors: Patricia Grob / Michael J Cruse / Carla Inouye / Marian Peris / Pawel A Penczek / Robert Tjian / Eva Nogales
DateDeposition: Feb 24, 2006 / Header (metadata) release: Feb 28, 2006 / Map release: Feb 28, 2007 / Last update: Aug 31, 2011

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.010946
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.010946
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_1196.map.gz (map file in CCP4 format, 2077 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
81 pix
5.06 Å/pix.
= 409.86 Å
81 pix
5.06 Å/pix.
= 409.86 Å
81 pix
5.06 Å/pix.
= 409.86 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.06 Å
Density
Contour Level:0.00785, 0.010946 (movie #1):
Minimum - Maximum-0.0390187 - 0.0942887
Average (Standard dev.)0.000285695 (0.00504258)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions818181
Origin000
Limit808080
Spacing818181
CellA=B=C: 409.86 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.065.065.06
M x/y/z818181
origin x/y/z0.0000.0000.000
length x/y/z409.860409.860409.860
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS818181
D min/max/mean-0.0390.0940.000

-
Supplemental data

-
Sample components

-
Entire Human TFIID

EntireName: Human TFIID
Details: The sample was prepared from a single preparation of TFIID, immunopurified from HeLa cell nuclear extrats (TAF130 antibody)
Number of components: 1
MassTheoretical: 1000 kDa / Experimental: 1000 kDa / Measured by: Chromatography, sequence

-
Component #1: protein, TFIID

ProteinName: TFIIDTranscription factor II D / Recombinant expression: Yes
MassTheoretical: 1000 kDa / Experimental: 1000 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: HeLa
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: HeLa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.025 mg/ml
Buffer solution: 25mM HEPES, 0.1 mM EDTA, 12.5mM MgCl2, 200mM KCl, 0.03% NP 40
pH: 7.9
Support film400 mesh copper grid with holey carbon
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 95 %
Details: Vitrification instrument: Vitrobot. rince once with sample buffer before blotting

-
Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50200 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 5000 nm
Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 90 K
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 90 / Scanner: OTHER / Sampling size: 12.7 microns / Bit depth: 14

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3447 / Details: additional continuous thin carbon layer / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: simultaneous iterative reconstruction technique / Software: Spider, IMAGIC / CTF correction: whole micrograph / Resolution: 35 Å / Resolution method: FSC 0.5 / Euler angles: SPIDER, theta 90 degrees, phi 359.9
Details: group 2 obtained by claculating 3D variance and 2D classification in high variance mask

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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