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- PDB-7apk: Structure of the human THO - UAP56 complex -

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Basic information

Entry
Database: PDB / ID: 7apk
TitleStructure of the human THO - UAP56 complex
Components
  • (THO complex subunit ...) x 6
  • Spliceosome RNA helicase DDX39B
  • THOC2 anchor (putative)
KeywordsGENE REGULATION / mRNA / nucleocytoplasmic transport / R-loop / gene expression
Function / homology
Function and homology information


THO complex / THO complex part of transcription export complex / primitive hemopoiesis / transcription export complex / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / mRNA 3'-end processing / ATP-dependent activity, acting on RNA ...THO complex / THO complex part of transcription export complex / primitive hemopoiesis / transcription export complex / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / ATP-dependent protein binding / U4 snRNA binding / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of DNA-templated transcription, elongation / U4 snRNP / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / generation of neurons / spliceosomal complex assembly / monocyte differentiation / blastocyst development / neuron development / RHOBTB2 GTPase cycle / U6 snRNA binding / mRNA export from nucleus / mRNA Splicing - Major Pathway / RNA splicing / regulation of DNA-templated transcription elongation / central nervous system development / spliceosomal complex / cell morphogenesis / mRNA processing / nuclear matrix / mRNA splicing, via spliceosome / 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 / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / 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 ...THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / 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 / Eukaryotic translation initiation factor eIF2A / 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 / DEAD/DEAH box helicase domain / 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 / 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
THO complex subunit 5 homolog / Spliceosome RNA helicase DDX39B / THO complex subunit 7 homolog / THO complex subunit 6 homolog / 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: 3.3 Å
AuthorsHohmann, U. / Puehringer, T. / Plaschka, C.
Funding support Austria, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationP2GEP3_188343 Austria
CitationJournal: Elife / Year: 2020
Title: Structure of the human core transcription-export complex reveals a hub for multivalent interactions.
Authors: Thomas Pühringer / Ulrich Hohmann / Laura Fin / Belén Pacheco-Fiallos / Ulla Schellhaas / Julius Brennecke / Clemens Plaschka /
Abstract: The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and ...The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and licenses mRNA for nuclear export by loading the export factor NXF1-NXT1. How TREX integrates these marks and achieves high selectivity for mature mRNA is poorly understood. Here, we report the cryo-electron microscopy structure of the human THO-UAP56/DDX39B complex at 3.3 Å resolution. The seven-subunit THO-UAP56/DDX39B complex multimerizes into a 28-subunit tetrameric assembly, suggesting that selective recognition of mature mRNA is facilitated by the simultaneous sensing of multiple, spatially distant mRNA regions and maturation marks. Two UAP56/DDX39B RNA helicases are juxtaposed at each end of the tetramer, which would allow one bivalent ALYREF protein to bridge adjacent helicases and regulate the TREX-mRNA interaction. Our structural and biochemical results suggest a conserved model for TREX complex function that depends on multivalent interactions between proteins and mRNA.
History
DepositionOct 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
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
M: THO complex subunit 5 homolog
N: THO complex subunit 6 homolog
O: THO complex subunit 7 homolog
P: Spliceosome RNA helicase DDX39B
X: THOC2 anchor (putative)
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
m: THO complex subunit 5 homolog
n: THO complex subunit 6 homolog
o: THO complex subunit 7 homolog
p: Spliceosome RNA helicase DDX39B
x: THOC2 anchor (putative)


Theoretical massNumber of molelcules
Total (without water)1,836,84330
Polymers1,836,84330
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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THO complex subunit ... , 6 types, 24 molecules AIaiBJbjCKckEMemFNfnGOgo

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


Mass: 81138.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC1, HPR1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q96FV9
#2: Protein
THO complex subunit 2 / Tho2 / hTREX120


Mass: 141584.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC2, CXorf3 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q8NI27
#3: Protein
THO complex subunit 3 / Tho3 / TEX1 homolog / hTREX45


Mass: 43279.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC3 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q96J01
#4: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC5, C22orf19, KIAA0983 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q13769
#5: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC6, WDR58, PSEC0006 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q86W42
#6: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC7, NIF3L1BP1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6I9Y2

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Protein / Protein/peptide , 2 types, 6 molecules HPhpXx

#7: 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: 51612.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX39B, BAT1, UAP56 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q13838, RNA helicase
#8: Protein/peptide THOC2 anchor (putative)


Mass: 3166.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5

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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

Component
IDNameTypeEntity IDParent-IDSource
1THO - UAP56COMPLEXall0MULTIPLE SOURCES
2THO complexCOMPLEX#1-#6, #81RECOMBINANT
3Spliceosome RNA helicase DDX39BCOMPLEX#71RECOMBINANT
Molecular weightValue: 1.836 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Trichoplusia ni (cabbage looper)7111Hi5
33Escherichia coli (E. coli)562BL21 DE3 RIL
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHepesC8H18N2O4S1
250 mMpotassium chlorideKCl1
31 mMTCEPC9H15O6P1
42 %GlycerolC3H8O31
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingAverage exposure time: 3.8 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 26303

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Processing

EM software
IDNameVersionCategory
4Warp1.07CTF correction
7Coot0.8.9model fitting
9PHENIX1.13model refinement
12RELION3.1classification
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1570265
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195098 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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