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- EMDB-17464: EM structure of endogenous TREX complex from S. cerevisiae -

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Basic information

Entry
Database: EMDB / ID: EMD-17464
TitleEM structure of endogenous TREX complex from S. cerevisiae
Map data
Sample
  • Complex: Endogenous TREX complex from S. cerevisiae
Keywordstranscription / mRNA export / protein complex / TREX / NUCLEAR PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsKern C / Straesser K
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)772049European Union
CitationJournal: RNA / Year: 2023
Title: Cross-linking mass spectrometric analysis of the endogenous TREX complex from .
Authors: Carina Kern / Christin Radon / Wolfgang Wende / Alexander Leitner / Katja Sträßer /
Abstract: The conserved TREX complex has multiple functions in gene expression such as transcription elongation, 3' end processing, mRNP assembly and nuclear mRNA export as well as the maintenance of genomic ...The conserved TREX complex has multiple functions in gene expression such as transcription elongation, 3' end processing, mRNP assembly and nuclear mRNA export as well as the maintenance of genomic stability. In , TREX is composed of the pentameric THO complex, the DEAD-box RNA helicase Sub2, the nuclear mRNA export adaptor Yra1, and the SR-like proteins Gbp2 and Hrb1. Here, we present the structural analysis of the endogenous TREX complex of purified from its native environment. To this end, we used cross-linking mass spectrometry to gain structural information on regions of the complex that are not accessible to classical structural biology techniques. We also used negative-stain electron microscopy to investigate the organization of the cross-linked complex used for XL-MS by comparing our endogenous TREX complex with recently published structural models of recombinant THO-Sub2 complexes. According to our analysis, the endogenous yeast TREX complex preferentially assembles into a dimer.
History
DepositionMay 26, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17464.png

Downloads & links

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Map

FileDownload / File: emd_17464.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 224 pix.
= 568.96 Å		2.54 Å/pix.
x 224 pix.
= 568.96 Å		2.54 Å/pix.
x 224 pix.
= 568.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.7877948 - 3.7868242
Average (Standard dev.)-0.006753798 (±0.10485513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 568.95996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17464_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_17464_half_map_2.map
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Sample components

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Entire : Endogenous TREX complex from S. cerevisiae

EntireName: Endogenous TREX complex from S. cerevisiae
Components
  • Complex: Endogenous TREX complex from S. cerevisiae

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Supramolecule #1: Endogenous TREX complex from S. cerevisiae

SupramoleculeName: Endogenous TREX complex from S. cerevisiae / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22024
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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