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- EMDB-18980: Structure of a human TREX complex (with the THO tetramer). -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-18980
TitleStructure of a human TREX complex (with the THO tetramer).
Map dataStructure of the human TREX complex (full THO tetramer), map.
Sample
  • Complex: Human TREX complex (THO - UAP56 - ALYREF N)
KeywordsmRNA export / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.89 Å
AuthorsHohmann U / Pacheco-Fiallos B / Plaschka C
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
H2020 Marie Curie Actions of the European Commission896416European Union
European Molecular Biology Organization (EMBO)ALTF_1175-2019European Union
CitationJournal: To Be Published
Title: A molecular switch orchestrates the export of human messenger RNA
Authors: Hohmann U / Pacheco-Fiallos B / Brennecke J / Plaschka C
History
DepositionNov 25, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18980.png

Downloads & links

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Map

FileDownload / File: emd_18980.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the human TREX complex (full THO tetramer), map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 352 pix.
= 436.48 Å		1.24 Å/pix.
x 352 pix.
= 436.48 Å		1.24 Å/pix.
x 352 pix.
= 436.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.735
Minimum - Maximum-1.7292589 - 3.8253074
Average (Standard dev.)0.025341872 (±0.12867723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 436.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Structure of the human TREX complex (full THO tetramer), half map B.

Fileemd_18980_half_map_1.map
AnnotationStructure of the human TREX complex (full THO tetramer), half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of the human TREX complex (full THO tetramer), half map A.

Fileemd_18980_half_map_2.map
AnnotationStructure of the human TREX complex (full THO tetramer), half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human TREX complex (THO - UAP56 - ALYREF N)

EntireName: Human TREX complex (THO - UAP56 - ALYREF N)
Components
  • Complex: Human TREX complex (THO - UAP56 - ALYREF N)

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Supramolecule #1: Human TREX complex (THO - UAP56 - ALYREF N)

SupramoleculeName: Human TREX complex (THO - UAP56 - ALYREF N) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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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: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.25 µm / Nominal defocus min: 0.75 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204147
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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