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- PDB-8u8d: Cryo-EM structure of the TREX-2 complex in complex with the N-ter... -

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Basic information

Entry
Database: PDB / ID: 8u8d
TitleCryo-EM structure of the TREX-2 complex in complex with the N-terminal motif of Sub2
Components
  • 26S proteasome complex subunit SEM1
  • Nuclear mRNA export factor
  • RNA helicase
  • THP1 isoform 1
KeywordsRNA BINDING PROTEIN / mRNA nuclear export
Function / homology: / : / : / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsClarke, B.P. / Xie, Y. / Ren, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133743 United States
CitationJournal: Structure / Year: 2025
Title: Structures and mRNP remodeling mechanism of the TREX-2 complex.
Authors: Yihu Xie / Bradley P Clarke / Dongqi Xie / Menghan Mei / Prasanna Bhat / Pate S Hill / Alexia E Angelos / Tolga Çağatay / Mariam Haider / Scott E Collier / Melissa G Chambers / Vasilisa ...Authors: Yihu Xie / Bradley P Clarke / Dongqi Xie / Menghan Mei / Prasanna Bhat / Pate S Hill / Alexia E Angelos / Tolga Çağatay / Mariam Haider / Scott E Collier / Melissa G Chambers / Vasilisa Aksenova / Mary Dasso / Beatriz M A Fontoura / Yi Ren /
Abstract: mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before ...mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before export to the cytoplasm, mRNPs undergo dynamic remodeling governed by the DEAD-box helicase DDX39B (yeast Sub2). DDX39B/Sub2 primarily functions in the nucleus and leaves the mRNP prior to export through the nuclear pore complex; however, the underlying mechanisms remain elusive. Here, we identify the conserved TREX-2 complex as the long-sought factor that facilitates DDX39B/Sub2 to complete the mRNP remodeling cycle. Our crystallographic and cryoelectron microscopy (cryo-EM) analyses demonstrate that TREX-2 modulates the activities of DDX39B/Sub2 through multiple interactions. Critically, a conserved "trigger loop" from TREX-2 splits the two RecA domains of DDX39B/Sub2 and promotes the removal of DDX39B/Sub2 from mRNP. Our findings suggest that TREX-2 coordinates with DDX39B/Sub2 and the human export receptor NXF1-NXT1 (yeast Mex67-Mtr2) to complete the final steps of nuclear mRNP assembly.
History
DepositionSep 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear mRNA export factor
B: THP1 isoform 1
C: 26S proteasome complex subunit SEM1
D: RNA helicase


Theoretical massNumber of molelcules
Total (without water)171,4444
Polymers171,4444
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Nuclear mRNA export factor


Mass: 57800.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SAC3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H8UN65
#2: Protein THP1 isoform 1


Mass: 52734.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: THP1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4BWR8
#3: Protein 26S proteasome complex subunit SEM1


Mass: 10397.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEM1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q1X7
#4: Protein RNA helicase


Mass: 50512.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUB2, GI527_G0000845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7I9D9F6, RNA helicase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TREX-2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 56.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 419645 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 113.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317908
ELECTRON MICROSCOPYf_angle_d0.391110705
ELECTRON MICROSCOPYf_chiral_restr0.03641186
ELECTRON MICROSCOPYf_plane_restr0.00271378
ELECTRON MICROSCOPYf_dihedral_angle_d9.33012996

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