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- EMDB-54283: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex, Map A -

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Basic information

Entry
Database: EMDB / ID: EMD-54283
TitleHuman UAP56-RNA - SAC3D1-PCID2-SEM1 complex, Map A
Map dataMap A of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
Sample
  • Complex: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
    • Complex: Human SAC3D1-PCID2-SEM1 complex
    • Complex: Human UAP56-RNA complex
KeywordsmRNA export / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 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: 2026
Title: Molecular basis of polyadenylated RNA fate determination in the nucleus.
Authors: Andrii Bugai / Ulrich Hohmann / Ana Lorenzo / Max Graf / Laura Fin / Jérôme O Rouvière / Laszlo Tirian / Yuhui Dou / Marion Le Rest / Patrik Polák / Dennis Johnsen / Lis Jakobsen / Jens ...Authors: Andrii Bugai / Ulrich Hohmann / Ana Lorenzo / Max Graf / Laura Fin / Jérôme O Rouvière / Laszlo Tirian / Yuhui Dou / Marion Le Rest / Patrik Polák / Dennis Johnsen / Lis Jakobsen / Jens Skorstengaard Andersen / Julius Brennecke / Clemens Plaschka / Torben Heick Jensen /
Abstract: Eukaryotic genomes generate a plethora of polyadenylated (pA) RNAs, which are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA RNPs, including ...Eukaryotic genomes generate a plethora of polyadenylated (pA) RNAs, which are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA RNPs, including protein-coding RNPs, are exported to the cytoplasm, whereas transcripts within non-functional pA RNPs are degraded in the nucleus. How cells distinguish these opposing fates remains unknown. The DExD-box ATPase UAP56 (also known as DDX39B) is a central component of functional pA RNPs, and promotes their docking to the nuclear pore complex-anchored TREX-2, which triggers transcript release from UAP56 to facilitate export. Here we reveal that the poly(A) tail exosome targeting (PAXT) connection binds a TREX-2-like module, which releases pA RNAs from UAP56 for decay by the nuclear exosome. The core of this module consists of a LENG8-PCID2-SEM1 trimer, which we show is structurally and biochemically equivalent to the central GANP-PCID2-SEM1 trimer of TREX-2. Mutagenesis and transcriptomic data demonstrate that the nuclear fate of pA RNPs is governed by the contending actions of nucleoplasmic PAXT and nuclear pore complex-associated TREX-2, which interpret RNA-bound UAP56 as a signal for RNA decay or export, respectively. As RNA targets of PAXT are generally short and intron-poor, we propose an overall model for pA RNP fate determination whereby the distinct sub-nuclear localizations of PAXT and TREX-2 govern the degradation of short non-functional pA RNAs while allowing export of their longer and functional counterparts.
History
DepositionJul 6, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54283.png

Downloads & links

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Map

FileDownload / File: emd_54283.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap A of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 256 pix.
= 229.888 Å		0.9 Å/pix.
x 256 pix.
= 229.888 Å		0.9 Å/pix.
x 256 pix.
= 229.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.898 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.49694726 - 0.7731855
Average (Standard dev.)0.0002054281 (±0.018676762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 229.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Map A/ half map 2 of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex

Fileemd_54283_half_map_1.map
AnnotationMap A/ half map 2 of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map A/ half map 1 of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex

Fileemd_54283_half_map_2.map
AnnotationMap A/ half map 1 of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
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-RNA - SAC3D1-PCID2-SEM1 complex

EntireName: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
Components
  • Complex: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
    • Complex: Human SAC3D1-PCID2-SEM1 complex
    • Complex: Human UAP56-RNA complex

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Supramolecule #1: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex

SupramoleculeName: Human UAP56-RNA - SAC3D1-PCID2-SEM1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human SAC3D1-PCID2-SEM1 complex

SupramoleculeName: Human SAC3D1-PCID2-SEM1 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human UAP56-RNA complex

SupramoleculeName: Human UAP56-RNA complex / type: complex / ID: 3 / Parent: 1 / 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

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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 129495
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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