[English] 日本語
Yorodumi
- EMDB-18980: Structure of a human TREX complex (with the THO tetramer). -

+
Open data


ID or keywords:

Loading...

-
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: Nature / Year: 2025
Title: An ATP-gated molecular switch orchestrates human mRNA export.
Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alexander W Phillips / Daria Riabov-Bassat / Rupert Faraway / Thomas ...Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alexander W Phillips / Daria Riabov-Bassat / Rupert Faraway / Thomas Pühringer / Michael-Florian Szalay / Elisabeth Roitinger / Julius Brennecke / Clemens Plaschka /
Abstract: The nuclear export of mRNA is an important step in eukaryotic gene expression. Despite recent molecular insights into how newly transcribed mRNAs are packaged into ribonucleoprotein complexes (mRNPs) ...The nuclear export of mRNA is an important step in eukaryotic gene expression. Despite recent molecular insights into how newly transcribed mRNAs are packaged into ribonucleoprotein complexes (mRNPs), the subsequent events that govern mRNA export are poorly understood. Here we uncover the molecular basis underlying key events of human mRNA export, including the remodelling of mRNP-bound transcription-export complexes (TREX), the formation of export-competent mRNPs, the docking of mRNPs at the nuclear pore complex (NPC), and the release of mRNPs at the NPC to initiate their export. Our biochemical and structural data show that the ATPase UAP56 (also known as DDX39) acts as a central molecular switch that directs nucleoplasmic mRNPs from TREX to NPC-anchored TREX-2 complexes through its ATP-gated mRNA-binding cycle. Collectively, these findings establish a mechanistic framework for a general and evolutionarily conserved mRNA export pathway.
History
DepositionNov 25, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18980.png

Downloads & links

-
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 °

-
Supplemental data

-
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)

-
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)

-
Sample components

-
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)

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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