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- EMDB-42021: Cryo-EM structure of the TREX-2 complex in complex with the N-ter... -

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Basic information

Entry
Database: EMDB / ID: EMD-42021
TitleCryo-EM structure of the TREX-2 complex in complex with the N-terminal motif of Sub2
Map datastructure of an mRNA export machinery
Sample
  • Complex: TREX-2 complex
    • Protein or peptide: Nuclear mRNA export factor
    • Protein or peptide: THP1 isoform 1
    • Protein or peptide: 26S proteasome complex subunit SEM1
    • Protein or peptide: RNA helicase
KeywordsmRNA nuclear export / RNA BINDING PROTEIN
Function / homology: / : / : / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 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)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, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42021.png

Downloads & links

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Map

FileDownload / File: emd_42021.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of an mRNA export machinery
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 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: 0.1
Minimum - Maximum-0.20071928 - 0.4426641
Average (Standard dev.)0.00032404848 (±0.011746872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_42021_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_42021_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TREX-2 complex

EntireName: TREX-2 complex
Components
  • Complex: TREX-2 complex
    • Protein or peptide: Nuclear mRNA export factor
    • Protein or peptide: THP1 isoform 1
    • Protein or peptide: 26S proteasome complex subunit SEM1
    • Protein or peptide: RNA helicase

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Supramolecule #1: TREX-2 complex

SupramoleculeName: TREX-2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Nuclear mRNA export factor

MacromoleculeName: Nuclear mRNA export factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 57.800023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSKSQQP LQNLSHSPSY TENKPDKKKK YMINDAKTIQ LVGPLISSPD NLGFQKRSHK ARELPRFLIN QEPQLEKRAF VQDPWDKAN QEKMISLEES IDDLNELYET LKKMRNTERS IMEEKGLVDK ADSAKDLYDA IVFQGTCLDM CPTFERSRRN V EYTVYSYE ...String:
GAMGSKSQQP LQNLSHSPSY TENKPDKKKK YMINDAKTIQ LVGPLISSPD NLGFQKRSHK ARELPRFLIN QEPQLEKRAF VQDPWDKAN QEKMISLEES IDDLNELYET LKKMRNTERS IMEEKGLVDK ADSAKDLYDA IVFQGTCLDM CPTFERSRRN V EYTVYSYE KNQPNDKKAS RTKALKVFAR PAAAAAPPLP SDVRPPHILV KTLDYIVDNL LTTLPESEGF LWDRMRSIRQ DF TYQNYSG PEAVDCNERI VRIHLLILHI MVKSNVEFSL QQELEQLHKS LITLSEIYDD VRSSGGTCPN EAEFRAYALL SKI RDPQYD ENIQRLPKHI FQDKLVQMAL CFRRVISNSA YTERGFVKTE NCLNFYARFF QLMQSPSLPL LMGFFLQMHL TDIR FYALR ALSHTLNKKH KPIPFIYLEN MLLFNNRQEI IEFCNYYSIE IINGDAADLK TLQHYSHKLS ETQPLKKTYL TCLER RLQK TTYKGLINGG EDN

UniProtKB: UNIPROTKB: A0A8H8UN65

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Macromolecule #2: THP1 isoform 1

MacromoleculeName: THP1 isoform 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 52.73482 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDMANQLLDE LAHGNFSHLT LNLSQNGREI AILQKQLTGF DDKQLETFVE QHPAMPNDTR FKIMCTSFLN YARDVDPWSA WSSSDLIFE FYQCLINCLI NDNAPHIEML IPVATRETEF IINLAGKLDS FHLQLHTRSH QFLSHISSIL SRLFNSIKPP R GNASSTNI ...String:
MDMANQLLDE LAHGNFSHLT LNLSQNGREI AILQKQLTGF DDKQLETFVE QHPAMPNDTR FKIMCTSFLN YARDVDPWSA WSSSDLIFE FYQCLINCLI NDNAPHIEML IPVATRETEF IINLAGKLDS FHLQLHTRSH QFLSHISSIL SRLFNSIKPP R GNASSTNI PGKQRILLYL VNKLNNIYFR IESPQLCSNI FKNFQPKSML AHFNEYQLDQ QIEYRYLLGR YYLLNSQVHN AF VQFNEAF QSLLNLPLTN QAITRNGTRI LNYMIPTGLI LGKMVKWGPL RPFLSQETID NWSVLYKHVR YGNIQGVSLW LRQ NERHLC ARQLLIVLLE KLPMVTYRNL IKTVIKSWTT EWGQNKLPYS LIERVLQLSI GPTFEDPGAQ EITIYNGIHS PKNV ENVLV TLINLGLLRA NCFPQLQLCV VKKTTMIQEI VPPVNERITK MFPAHSHVLW

UniProtKB: UNIPROTKB: A0A8H4BWR8

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Macromolecule #3: 26S proteasome complex subunit SEM1

MacromoleculeName: 26S proteasome complex subunit SEM1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.397102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTDVAAAQA QSKIDLTKKK NEEINKKSLE EDDEFEDFPI DTWANGETIK SNAVTQTNIW EENWDDVEVD DDFTNELKAE LDRYKRENQ

UniProtKB: UNIPROTKB: A0A6A5Q1X7

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Macromolecule #4: RNA helicase

MacromoleculeName: RNA helicase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.512051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHEGEEDLL EYSDNEQEIQ IDASKAAEAG ETGAATSATE GDNNNNTAAG DKKGSYVGIH STGFKDFLLK PELSRAIIDC GFEHPSEVQ QHTIPQSIHG TDVLCQAKSG LGKTAVFVLS TLQQL(PBF)PVPG EVAVVVICNA RELAYQIRNE YLRFSKY MP DVKTAVFYGG ...String:
MSHEGEEDLL EYSDNEQEIQ IDASKAAEAG ETGAATSATE GDNNNNTAAG DKKGSYVGIH STGFKDFLLK PELSRAIIDC GFEHPSEVQ QHTIPQSIHG TDVLCQAKSG LGKTAVFVLS TLQQL(PBF)PVPG EVAVVVICNA RELAYQIRNE YLRFSKY MP DVKTAVFYGG TPISKDAELL KNKDTAPHIV VATPGRLKAL VREKYIDLSH VKNFVIDECD KVLEELDMRR DVQEIFRA T PRDKQVMMFS ATLSQEIRPI CRRFLQNPLE IFVDDEAKLT LHGLQQYYIK LEEREKNRKL AQLLDDLEFN QVIIFVKST TRANELTKLL NASNFPAITV HGHMKQEERI ARYKAFKDFE KRICVSTDVF GRGIDIERIN LAINYDLTNE ADQYLHRVGR AGRFGTKGL AISFVSSKED EEVLAKIQER FDVKIAEFPE EGIDPSTYLN N

UniProtKB: UNIPROTKB: A0A7I9D9F6

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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: 56.4 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ubp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 419645
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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