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- PDB-8r7l: Cryo-EM structure of the human TREX complex -

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Basic information

Entry
Database: PDB / ID: 8r7l
TitleCryo-EM structure of the human TREX complex
Components
  • Spliceosome RNA helicase DDX39B
  • THO complex subunit 1
  • THO complex subunit 2
  • THO complex subunit 3
  • THO complex subunit 4
KeywordsGENE REGULATION / mRNA export
Function / homology
Function and homology information


THO complex / THO complex part of transcription export complex / transcription export complex / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / ATP-dependent activity, acting on RNA / mRNA 3'-end processing ...THO complex / THO complex part of transcription export complex / transcription export complex / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / ATP-dependent activity, acting on RNA / mRNA 3'-end processing / ATP-dependent protein binding / Transport of Mature mRNA Derived from an Intronless Transcript / U4 snRNA binding / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U4 snRNP / stem cell division / poly(A)+ mRNA export from nucleus / generation of neurons / spliceosomal complex assembly / blastocyst development / U6 snRNA binding / neuron development / RHOBTB2 GTPase cycle / mRNA export from nucleus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / nuclear matrix / cell morphogenesis / mRNA processing / osteoblast differentiation / negative regulation of neuron projection development / regulation of gene expression / RNA helicase activity / nuclear speck / RNA helicase / mRNA binding / apoptotic process / signal transduction / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
THOC3 beta-propeller domain / Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / TREX component Tex1/THOC3 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 ...THOC3 beta-propeller domain / Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / TREX component Tex1/THOC3 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Transcription factor/nuclear export subunit protein 2 / Transcription- and export-related complex subunit / THO complex subunit 2 N-terminus / THO complex, subunit THOC1 / THO complex subunit 1 transcription elongation factor / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / G-protein beta WD-40 repeat / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Spliceosome RNA helicase DDX39B / THO complex subunit 4 / THO complex subunit 2 / THO complex subunit 1 / THO complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.12 Å
AuthorsHohmann, U. / Pacheco-Fiallos, B. / Plaschka, C.
Funding supportEuropean Union, 3items
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 mRNA export.
Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alexander W Phillips / Daria Riabov-Bassat / Rupert Faraway / Thomas ...Authors: Ulrich Hohmann / Max Graf / László Tirián / Belén Pacheco-Fiallos / Ulla Schellhaas / Laura Fin / Dominik Handler / Alexander W Phillips / Daria Riabov-Bassat / Rupert Faraway / Thomas Pühringer / Michael-Florian Szalay / Elisabeth Roitinger / Julius Brennecke / Clemens Plaschka /
Abstract: The nuclear export of 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 nuclear export of 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 remodelling 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 UAP56 (also known as DDX39) 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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Spliceosome RNA helicase DDX39B
A: THO complex subunit 1
B: THO complex subunit 2
C: THO complex subunit 3
D: THO complex subunit 4


Theoretical massNumber of molelcules
Total (without water)365,9475
Polymers365,9475
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Spliceosome RNA helicase DDX39B / 56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B- ...56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B-associated transcript 1 protein


Mass: 49056.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX39B, BAT1, UAP56 / Plasmid: plasmid 006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13838, RNA helicase
#2: Protein THO complex subunit 1 / Tho1 / Nuclear matrix protein p84 / p84N5 / hTREX84


Mass: 75752.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC1, HPR1 / Plasmid: CP009 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q96FV9
#3: Protein THO complex subunit 2 / Tho2 / hTREX120


Mass: 183087.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC2, CXorf3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NI27
#4: Protein THO complex subunit 3 / Tho3 / TEX1 homolog / hTREX45


Mass: 38817.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96J01
#5: Protein THO complex subunit 4 / Tho4 / Ally of AML-1 and LEF-1 / Aly/REF export factor / Transcriptional coactivator Aly/REF / bZIP- ...Tho4 / Ally of AML-1 and LEF-1 / Aly/REF export factor / Transcriptional coactivator Aly/REF / bZIP-enhancing factor BEF


Mass: 19233.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALYREF, ALY, BEF, THOC4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86V81
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: Human TREX complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1250 nm / Nominal defocus min: 750 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204147 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00815247
ELECTRON MICROSCOPYf_angle_d1.61420581
ELECTRON MICROSCOPYf_dihedral_angle_d7.4931989
ELECTRON MICROSCOPYf_chiral_restr0.0832322
ELECTRON MICROSCOPYf_plane_restr0.0122619

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