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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 / mRNA 3'-end processing / ATP-dependent activity, acting on RNA ...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 / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / Transport of Mature mRNA Derived from an Intronless Transcript / U4 snRNA binding / ATP-dependent protein binding / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNP / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / stem cell division / generation of neurons / spliceosomal complex assembly / blastocyst development / U6 snRNA binding / neuron development / mRNA export from nucleus / RHOBTB2 GTPase cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / cell morphogenesis / 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 / cytoplasm / cytosol
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: To Be Published
Title: A molecular switch orchestrates the export of human messenger RNA
Authors: Hohmann, U. / Pacheco-Fiallos, B. / Brennecke, J. / Plaschka, C.
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

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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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