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- PDB-7v2y: cryo-EM structure of yeast THO complex with Sub2 -

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Basic information

Entry
Database: PDB / ID: 7v2y
Titlecryo-EM structure of yeast THO complex with Sub2
Components
  • (THO complex subunit ...) x 4
  • ATP-dependent RNA helicase SUB2
  • Protein TEX1
KeywordsTRANSCRIPTION / RNA transcription
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 / subtelomeric heterochromatin formation ...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 / subtelomeric heterochromatin formation / mRNA export from nucleus / transcription-coupled nucleotide-excision repair / stress granule assembly / spliceosomal complex / transcription elongation by RNA polymerase II / 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 / Transcription factor/nuclear export subunit protein 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 / 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 / WD domain, G-beta repeat / 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
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: 3.4 Å
AuthorsChen, C. / Tan, M. / Wu, Z. / Wu, J. / Lei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Bull (Beijing) / Year: 2021
Title: Structural and functional insights into R-loop prevention and mRNA export by budding yeast THO-Sub2 complex.
Authors: Cong Chen / Ming Tan / Zhenfang Wu / Yuebin Zhang / Fanyang He / Yanjia Lu / Shaobai Li / Mi Cao / Guohui Li / Jian Wu / Hong Cheng / Ming Lei /
History
DepositionAug 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THO complex subunit HPR1
B: THO complex subunit 2
C: Protein TEX1
D: THO complex subunit MFT1
E: THO complex subunit THP2
F: ATP-dependent RNA helicase SUB2


Theoretical massNumber of molelcules
Total (without water)445,1036
Polymers445,1036
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area43800 Å2
ΔGint-246 kcal/mol
Surface area132980 Å2

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Components

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THO complex subunit ... , 4 types, 4 molecules ABDE

#1: Protein THO complex subunit HPR1 / Hyperrecombination protein 1


Mass: 87938.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: HPR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17629
#2: Protein THO complex subunit 2 / THO complex subunit RLR1


Mass: 184163.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: THO2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53552
#4: Protein THO complex subunit MFT1 / Mitochondrial fusion target protein 1


Mass: 45055.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: MFT1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33441
#5: Protein THO complex subunit THP2


Mass: 30340.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: THP2, YHR167W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O13539

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Protein , 2 types, 2 molecules CF

#3: Protein Protein TEX1 / Trex component 1


Mass: 47229.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: TEX1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53851
#6: Protein ATP-dependent RNA helicase SUB2 / Suppressor of BRR1 protein 2


Mass: 50375.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SUB2 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07478, 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

Component
IDNameTypeEntity IDParent-IDSource
1THO-Sub2 ComplexCOMPLEXall0RECOMBINANT
2yeast THOCOMPLEX#1-#51RECOMBINANT
3Sub2COMPLEX#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae S288c (yeast)559292
32Saccharomyces cerevisiae S288c (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Spodoptera frugiperda (fall armyworm)7108
32Escherichia coli BL21(DE3) (bacteria)469008BL21(DE3)
Buffer solutionpH: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284361 / Symmetry type: POINT

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