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- EMDB-35718: RNA polymerase III pre-initiation complex open complex 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-35718
TitleRNA polymerase III pre-initiation complex open complex 2
Map dataRNA polymerase III pre-initiation complex open complex 2
Sample
  • Complex: RNA polymerase III pre-initiation complex open complex 2
KeywordsRNA polymerase III / SNAPC / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHou H / Jin Q / Ren Y / Wang Q / Xu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2023
Title: Structure of the SNAPc-bound RNA polymerase III preinitiation complex.
Authors: Haifeng Hou / Qianwei Jin / Yulei Ren / Zhenguo Chen / Qianmin Wang / Yanhui Xu /
History
DepositionMar 24, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35718.png

Downloads & links

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Map

FileDownload / File: emd_35718.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA polymerase III pre-initiation complex open complex 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 320 pix.
= 426.88 Å		1.33 Å/pix.
x 320 pix.
= 426.88 Å		1.33 Å/pix.
x 320 pix.
= 426.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.334 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.08521982 - 0.29226235
Average (Standard dev.)-0.000030355399 (±0.006676968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 426.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map-1

Fileemd_35718_half_map_1.map
Annotationhalf map-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map-2

Fileemd_35718_half_map_2.map
Annotationhalf map-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA polymerase III pre-initiation complex open complex 2

EntireName: RNA polymerase III pre-initiation complex open complex 2
Components
  • Complex: RNA polymerase III pre-initiation complex open complex 2

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Supramolecule #1: RNA polymerase III pre-initiation complex open complex 2

SupramoleculeName: RNA polymerase III pre-initiation complex open complex 2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1 MDa

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60982
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: OTHER

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