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- PDB-7aqo: yeast THO-Sub2 complex dimer -

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Basic information

Entry
Database: PDB / ID: 7aqo
Titleyeast THO-Sub2 complex dimer
Components
  • (THO complex subunit ...) x 3
  • BJ4_G0025130.mRNA.1.CDS.1
  • EM14S01-3B_G0007820.mRNA.1.CDS.1
  • TEX1 isoform 1
KeywordsRNA BINDING PROTEIN / yeast THO complex S. cerevisiae THO-Sub2 the transcription-export (TREX) complex
Function / homology
Function and homology information


nucleoplasmic THO complex / cellular response to azide / THO complex / THO complex part of transcription export complex / positive regulation of transcription elongation by RNA polymerase I / transcription export complex / Cdc73/Paf1 complex / mRNA 3'-end processing / positive regulation of transcription by RNA polymerase I / mRNA export from nucleus ...nucleoplasmic THO complex / cellular response to azide / THO complex / THO complex part of transcription export complex / positive regulation of transcription elongation by RNA polymerase I / transcription export complex / Cdc73/Paf1 complex / mRNA 3'-end processing / positive regulation of transcription by RNA polymerase I / mRNA export from nucleus / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair / stress granule assembly / spliceosomal complex / transcription elongation by RNA polymerase II / helicase activity / mRNA splicing, via spliceosome / mRNA processing / DNA recombination / molecular adaptor activity / nucleic acid binding / chromosome, telomeric region / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
THO complex subunit Thp2 / Tho complex subunit THP2 / : / THO complex subunit 7/Mft1 / TREX component Tex1/THOC3 / Tho complex subunit 7 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 ...THO complex subunit Thp2 / Tho complex subunit THP2 / : / THO complex subunit 7/Mft1 / TREX component Tex1/THOC3 / Tho complex subunit 7 / 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 / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / WD domain, G-beta repeat / 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 / 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
BJ4_G0002130.mRNA.1.CDS.1 / EM14S01-3B_G0007820.mRNA.1.CDS.1 / TEX1 isoform 1 / THO complex subunit 2 / THO complex subunit THP2 / THO complex subunit HPR1 / THO complex subunit MFT1 / THO complex subunit 2 / Protein TEX1 / ATP-dependent RNA helicase SUB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSchuller, S.K. / Schuller, J.M. / Prabu, R.J. / Baumgartner, M. / Bonneau, F. / basquin, J. / Conti, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC Advanced Investigator Grant EXORICO Germany
German Research Foundation (DFG)GRK1721, SFB/TRR 237 Germany
CitationJournal: Elife / Year: 2020
Title: Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex.
Authors: Sandra K Schuller / Jan M Schuller / J Rajan Prabu / Marc Baumgärtner / Fabien Bonneau / Jérôme Basquin / Elena Conti /
Abstract: The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to ...The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. How THO-containing complexes function at the mechanistic level is unclear. Here, we elucidated a 3.4 Å resolution structure of THO-Sub2 by cryo-electron microscopy. THO subunits Tho2 and Hpr1 intertwine to form a platform that is bound by Mft1, Thp2, and Tex1. The resulting complex homodimerizes in an asymmetric fashion, with a Sub2 molecule attached to each protomer. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis.
History
DepositionOct 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
G: THO complex subunit 2
H: THO complex subunit HPR1
K: TEX1 isoform 1
L: EM14S01-3B_G0007820.mRNA.1.CDS.1
A: THO complex subunit 2
B: THO complex subunit HPR1
E: TEX1 isoform 1
F: EM14S01-3B_G0007820.mRNA.1.CDS.1
J: BJ4_G0025130.mRNA.1.CDS.1
I: THO complex subunit MFT1
C: BJ4_G0025130.mRNA.1.CDS.1
D: THO complex subunit MFT1


Theoretical massNumber of molelcules
Total (without water)864,45112
Polymers864,45112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area77460 Å2
ΔGint-594 kcal/mol
Surface area245670 Å2
MethodPISA

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Components

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THO complex subunit ... , 3 types, 6 molecules GAHBID

#1: Protein THO complex subunit 2


Mass: 184450.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: THO2, GI526_G0004933 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5Q535, UniProt: P53552*PLUS
#2: Protein THO complex subunit HPR1 / Hyperrecombination protein 1


Mass: 84544.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HPR1, YDR138W, YD9302.14 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17629
#6: Protein THO complex subunit MFT1 / Mitochondrial fusion target protein 1


Mass: 45055.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MFT1, YML062C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33441

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Protein , 3 types, 6 molecules KELFJC

#3: Protein TEX1 isoform 1 / Y55_G0044670.mRNA.1.CDS.1


Mass: 42315.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TEX1, GI526_G0004829, PACBIOSEQ_LOCUS5457 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5Q4V2, UniProt: P53851*PLUS
#4: Protein EM14S01-3B_G0007820.mRNA.1.CDS.1 / HN1_G0007890.mRNA.1.CDS.1 / JXXY16.1_G0007900.mRNA.1.CDS.1 / SUB2 isoform 1 / SX2_G0007910.mRNA.1. ...HN1_G0007890.mRNA.1.CDS.1 / JXXY16.1_G0007900.mRNA.1.CDS.1 / SUB2 isoform 1 / SX2_G0007910.mRNA.1.CDS.1 / XXYS1_G0007860.mRNA.1.CDS.1


Mass: 45521.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast)
Gene: SUB2, GI526_G0000835, PACBIOSEQ_LOCUS934, PACBIOSEQ_LOCUS949, PACBIOSEQ_LOCUS951, PACBIOSEQ_LOCUS965
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5Q316, UniProt: Q07478*PLUS
#5: Protein BJ4_G0025130.mRNA.1.CDS.1 / HLJ1_G0025020.mRNA.1.CDS.1 / THP2 isoform 1 / Y55_G0025210.mRNA.1.CDS.1


Mass: 30340.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast)
Gene: THP2, GI526_G0002950, PACBIOSEQ_LOCUS3229, PACBIOSEQ_LOCUS3284, PACBIOSEQ_LOCUS3351
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5PZX4, UniProt: O13539*PLUS

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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: yeast THO-Sub2 complex dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 862 kDa/nm / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4GctfCTF correction
7PHENIXmodel fitting
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113076 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7APX

7apx


Accession code: 7APX / Source name: PDB / Type: experimental model

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