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- EMDB-47126: Cryo-EM map of the human TREX-2.1 complex bound to DDX39B(UAP56) -

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Basic information

Entry
Database: EMDB / ID: EMD-47126
TitleCryo-EM map of the human TREX-2.1 complex bound to DDX39B(UAP56)
Map dataCryo-EM map of the human TREX-2.1 complex bound to DDX39B(UAP56)
Sample
  • Complex: human TREX-2.1 complex(LENG8/PCID2/DSS1) and DDX39B
KeywordsmRNA nuclear export / TREX / TREX-2 / LENG8 / UAP56 / DDX39B / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsClarke BP / Xie Y / Ren Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural mechanism of DDX39B regulation by human TREX-2 and a related complex in mRNP remodeling.
Authors: Bradley P Clarke / Shengyan Gao / Menghan Mei / Dongqi Xie / Alexia E Angelos / Ashley Vazhavilla / Pate S Hill / Tolga Cagatay / Kimberly Batten / Jerry W Shay / Yihu Xie / Beatriz M A Fontoura / Yi Ren /
Abstract: Nuclear export of mRNAs in the form of messenger ribonucleoprotein particles (mRNPs) is an obligatory step for eukaryotic gene expression. The DEAD-box ATPase DDX39B (also known as UAP56) is a ...Nuclear export of mRNAs in the form of messenger ribonucleoprotein particles (mRNPs) is an obligatory step for eukaryotic gene expression. The DEAD-box ATPase DDX39B (also known as UAP56) is a multifunctional regulator of nuclear mRNPs. How DDX39B mediates mRNP assembly and export in a controlled manner remains elusive. Here, we identify a novel complex TREX-2.1 localized in the nucleus that facilitates the release of DDX39B from the mRNP. TREX-2.1 is composed of three subunits, LENG8, PCID2, and DSS1, and shares the latter two subunits with the nuclear pore complex-associated TREX-2 complex. Cryo-EM structures of TREX-2.1/DDX39B and TREX-2/DDX39B identify a conserved trigger loop in the LENG8 and GANP subunit of the respective TREX-2.1 and TREX-2 complex that is critical for DDX39B regulation. RNA sequencing from LENG8 knockdown cells shows that LENG8 influences the nucleocytoplasmic ratio of a subset of mRNAs with high GC content. Together, our findings lead to a mechanistic understanding of the functional cycle of DDX39B and its regulation by TREX-2 and TREX-2.1 in mRNP processing.
History
DepositionSep 25, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47126.png

Downloads & links

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Map

FileDownload / File: emd_47126.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the human TREX-2.1 complex bound to DDX39B(UAP56)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 236.16 Å		0.82 Å/pix.
x 288 pix.
= 236.16 Å		0.82 Å/pix.
x 288 pix.
= 236.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.2253759 - 0.36625165
Average (Standard dev.)-0.00027190786 (±0.00935098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 236.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_47126_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47126_half_map_2.map
AnnotationHalf 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 TREX-2.1 complex(LENG8/PCID2/DSS1) and DDX39B

EntireName: human TREX-2.1 complex(LENG8/PCID2/DSS1) and DDX39B
Components
  • Complex: human TREX-2.1 complex(LENG8/PCID2/DSS1) and DDX39B

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Supramolecule #1: human TREX-2.1 complex(LENG8/PCID2/DSS1) and DDX39B

SupramoleculeName: human TREX-2.1 complex(LENG8/PCID2/DSS1) and DDX39B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
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: OTHER / Details: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191817
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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