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- PDB-7znk: Structure of an endogenous human TREX complex bound to mRNA -

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Basic information

Entry
Database: PDB / ID: 7znk
TitleStructure of an endogenous human TREX complex bound to mRNA
Components
  • (THO complex subunit ...) x 7
  • RNA
  • Spliceosome RNA helicase DDX39B
KeywordsGENE REGULATION / transcription and export complex / TREX / RNA export / RNA packaging / RNA binding protein / gene expression
Function / homology
Function and homology information


THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / Transport of the SLBP independent Mature mRNA ...THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / C5-methylcytidine-containing RNA reader activity / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / ATP-dependent protein binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / ATP-dependent activity, acting on RNA / U4 snRNA 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 / generation of neurons / spliceosomal complex assembly / monocyte differentiation / blastocyst development / RHOBTB2 GTPase cycle / mRNA export from nucleus / neuron development / U6 snRNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / central nervous system development / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / osteoblast differentiation / Signaling by CSF1 (M-CSF) in myeloid cells / negative regulation of neuron projection development / regulation of gene expression / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / mRNA binding / apoptotic process / signal transduction / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / 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 subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal ...THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / 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 subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Tho complex subunit 7 / 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 / WD40-like beta propeller / WD40-like Beta Propeller Repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / 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 / Helicase conserved C-terminal domain / RNA-binding domain superfamily / 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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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
RNA / THO complex subunit 5 / Spliceosome RNA helicase DDX39B / THO complex subunit 7 / THO complex subunit 4 / THO complex subunit 6 / 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: 3.9 Å
AuthorsPacheco-Fiallos, F.B. / Vorlaender, M.K. / Plaschka, C.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
European Molecular Biology Organization (EMBO)623-2020European Union
CitationJournal: Nature / Year: 2023
Title: mRNA recognition and packaging by the human transcription-export complex.
Authors: Belén Pacheco-Fiallos / Matthias K Vorländer / Daria Riabov-Bassat / Laura Fin / Francis J O'Reilly / Farja I Ayala / Ulla Schellhaas / Juri Rappsilber / Clemens Plaschka /
Abstract: Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the ...Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.
History
DepositionApr 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: RNA
4: RNA
A: THO complex subunit 1
B: THO complex subunit 2
C: THO complex subunit 3
E: THO complex subunit 5 homolog
F: THO complex subunit 6 homolog
G: THO complex subunit 7 homolog
H: Spliceosome RNA helicase DDX39B
I: THO complex subunit 1
J: THO complex subunit 2
K: THO complex subunit 3
L: THO complex subunit 4
M: THO complex subunit 5 homolog
N: THO complex subunit 6 homolog
O: THO complex subunit 7 homolog
P: Spliceosome RNA helicase DDX39B
a: THO complex subunit 1
b: THO complex subunit 2
c: THO complex subunit 3
e: THO complex subunit 5 homolog
f: THO complex subunit 6 homolog
g: THO complex subunit 7 homolog
h: Spliceosome RNA helicase DDX39B
i: THO complex subunit 1
j: THO complex subunit 2
k: THO complex subunit 3
l: THO complex subunit 4
m: THO complex subunit 5 homolog
n: THO complex subunit 6 homolog
o: THO complex subunit 7 homolog
p: Spliceosome RNA helicase DDX39B


Theoretical massNumber of molelcules
Total (without water)2,002,52132
Polymers2,002,52132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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THO complex subunit ... , 7 types, 26 molecules AIaiBJbjCKckEMemFNfnGOgoLl

#2: Protein
THO complex subunit 1 / Tho1 / Nuclear matrix protein p84 / p84N5 / hTREX84


Mass: 75752.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96FV9
#3: Protein
THO complex subunit 2 / Tho2 / hTREX120


Mass: 183087.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NI27
#4: Protein
THO complex subunit 3 / Tho3 / TEX1 homolog / hTREX45


Mass: 38817.617 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96J01
#5: Protein
THO complex subunit 5 homolog / Functional spliceosome-associated protein 79 / fSAP79 / NF2/meningioma region protein pK1.3 / ...Functional spliceosome-associated protein 79 / fSAP79 / NF2/meningioma region protein pK1.3 / Placental protein 39.2 / PP39.2 / hTREX90


Mass: 78652.898 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13769
#6: Protein
THO complex subunit 6 homolog / Functional spliceosome-associated protein 35 / fSAP35 / WD repeat-containing protein 58


Mass: 37577.875 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86W42
#7: Protein
THO complex subunit 7 homolog / Functional spliceosome-associated protein 24 / fSAP24 / Ngg1-interacting factor 3-like protein 1- ...Functional spliceosome-associated protein 24 / fSAP24 / Ngg1-interacting factor 3-like protein 1-binding protein 1 / NIF3L1-binding protein 1 / hTREX30


Mass: 23782.014 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6I9Y2
#9: 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: 26934.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86V81

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RNA chain / Protein , 2 types, 6 molecules 24HPhp

#1: RNA chain RNA


Mass: 873.540 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#8: 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.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13838, RNA helicase

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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: endogenous human TREX-mRNA complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenConc.: 0.2 mg/ml / Embedding 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: FEI TITAN 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: 500 nm
Image recordingElectron dose: 60 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182534 / Symmetry type: POINT

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