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- EMDB-1195: Cryo-electron microscopy studies of human TFIID: conformational b... -

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Basic information

Entry
Database: EMDB / ID: EMD-1195
TitleCryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.
Map dataAverage 3D structure of human TFIID in solution (cryo-EM)
Sample
  • Sample: human TFIIDTranscription factor II D
  • Protein or peptide: TFIIDTranscription factor II D
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 32.0 Å
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 /
Abstract: The multisubunit transcription factor TFIID is essential for directing eukaryotic promoter recognition and mediating interactions with activators/cofactors during assembly of the preinitiation ...The multisubunit transcription factor TFIID is essential for directing eukaryotic promoter recognition and mediating interactions with activators/cofactors during assembly of the preinitiation complex. Despite its central role in transcription initiation and regulation, structural knowledge of the TFIID complex has so far been largely limited to electron microscopy studies of negatively stained samples. Here, we present a cryo-electron microscopy 3D reconstruction of the large endogenous human TFIID complex. The improved cryopreservation has allowed for a more detailed definition of the structural elements in the complex and for the detection, by an extensive statistical analysis of the data, of a conformational opening and closing of the cavity central to the TFIID architecture. We propose that these density rearrangements in the structure are a likely reflection of the plasticity of the interactions between TFIID and its many partner proteins.
History
DepositionFeb 23, 2006-
Header (metadata) releaseFeb 28, 2006-
Map releaseFeb 28, 2007-
UpdateAug 31, 2011-
Current statusAug 31, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009888
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.009888
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1195.gif

Downloads & links

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Map

FileDownload / File: emd_1195.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAverage 3D structure of human TFIID in solution (cryo-EM)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour Level1: 0.00701 / Movie #1: 0.009888
Minimum - Maximum-0.0259656 - 0.0837595
Average (Standard dev.)0.000289196 (±0.00447566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions818181
Spacing818181
CellA=B=C: 409.86 Å
α=β=γ: 90 °

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-0.0260.0840.000

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Supplemental data

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Sample components

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Entire : human TFIID

EntireName: human TFIIDTranscription factor II D
Components
  • Sample: human TFIIDTranscription factor II D
  • Protein or peptide: TFIIDTranscription factor II D

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Supramolecule #1000: human TFIID

SupramoleculeName: human TFIID / type: sample / ID: 1000
Details: The sample was prepared from a single preparation of TFIID, immunopurified from HeLa cell nuclear extrats (TAF130 antibody)
Number unique components: 1
Molecular weightExperimental: 1.0 MDa / Theoretical: 1.0 MDa / Method: Chromatography, sequence

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Macromolecule #1: TFIID

MacromoleculeName: TFIID / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: HeLa / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 1.0 MDa / Theoretical: 1.0 MDa
Recombinant expressionOrganism: HeLa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.025 mg/mL
BufferpH: 7.9
Details: 25mM HEPES, 0.1 mM EDTA, 12.5mM MgCl2, 200mM KCl, 0.03% NP 40
GridDetails: 400 mesh copper grid with holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 93 K / Instrument: OTHER
Details: Vitrification instrument: Vitrobot. rince once with sample buffer before blotting

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 90 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.7 µm / Number real images: 90 / Average electron dose: 16 e/Å2 / Bits/pixel: 14

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Image processing

CTF correctionDetails: whole micrograph
Final angle assignmentDetails: SPIDER, theta 90 degrees, phi 359.9
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, IMAGIC
Details: final reconstruction from 8016 single particles, refined by iterative projection matching
Number images used: 8016
Detailsadditional continuous thin carbon layer

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