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- EMDB-18981: Structure of the human UAP56 RecA1 RecA2 - TREX-2 complex -

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Entry
Database: EMDB / ID: EMD-18981
TitleStructure of the human UAP56 RecA1 RecA2 - TREX-2 complex
Map dataStructure of the human UAP56 RecA1 RecA2 - TREX-2 complex, map.
Sample
  • Complex: Human UAP56 - TREX-2 complex
    • Complex: Human TREX-2 complex middle domain
KeywordsmRNA export / nuclear pore basket / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsHohmann U / Graf M / 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 messenger RNA export.
Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alex W Philipps / Daria Riabov-Bassat / Rupert W Faraway / Thomas ...Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alex W Philipps / Daria Riabov-Bassat / Rupert W Faraway / Thomas Pühringer / Michael-Florian Szalay / Elisabeth Roitinger / Julius Brennecke / Clemens Plaschka /
Abstract: The nuclear export of messenger RNA (mRNA) is an important step in eukaryotic gene expression. Despite recent molecular insights into how newly transcribed mRNAs are packaged into ribonucleoprotein ...The nuclear export of messenger RNA (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 remodeling 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 DDX39/UAP56 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) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18981.png

Downloads & links

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Map

FileDownload / File: emd_18981.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the human UAP56 RecA1 RecA2 - TREX-2 complex, map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 224.512 Å		0.88 Å/pix.
x 256 pix.
= 224.512 Å		0.88 Å/pix.
x 256 pix.
= 224.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.877 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.049
Minimum - Maximum-0.306974 - 0.45010293
Average (Standard dev.)0.00045245717 (±0.015399795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 224.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Structure of the human UAP56 RecA1 RecA2 -...

Fileemd_18981_half_map_1.map
AnnotationStructure of the human UAP56 RecA1 RecA2 - TREX-2 complex, half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of the human UAP56 RecA1 RecA2 -...

Fileemd_18981_half_map_2.map
AnnotationStructure of the human UAP56 RecA1 RecA2 - TREX-2 complex, half map B.
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 UAP56 - TREX-2 complex

EntireName: Human UAP56 - TREX-2 complex
Components
  • Complex: Human UAP56 - TREX-2 complex
    • Complex: Human TREX-2 complex middle domain

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Supramolecule #1: Human UAP56 - TREX-2 complex

SupramoleculeName: Human UAP56 - TREX-2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human TREX-2 complex middle domain

SupramoleculeName: Human TREX-2 complex middle domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
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

Concentration0.7 mg/mL
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: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7412
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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